阅读说明：本技术 自组装诊断阵列平台 (Self-assembling diagnostic array platform ) 是由 R·博汉农 M·斯图尔特 D·罗布森 E·法雷尔 L·亨德森 N·麦克欧文 S·博汉农 于 2018-12-19 设计创作，主要内容包括：本公开文本涉及用于使用通用阵列平台检测样品中的核酸或抗原的方法和试剂盒。例如,可以通过以下方式检测核酸：使用引物对扩增来自样品的核酸的至少一部分,所述引物对包括第一引物和第二引物,所述第一引物包含标记和第一寡核苷酸序列,所述第一寡核苷酸序列与所述核酸的所述部分的第一链杂交,所述第二引物包含第二寡核苷酸序列,所述第二寡核苷酸序列与所述核酸的所述部分的第二链杂交；使存在时的所述扩增子与各自附着于固体支持物的多种单链寡核苷酸捕获序列接触；将胶体检测试剂施加至所述固体支持物；用洗涤溶液洗涤所述固体支持物；以及检测所述胶体检测试剂。本公开文本进一步涉及特异性捕获寡核苷酸序列和系链寡核苷酸序列。(The present disclosure relates to methods and kits for detecting nucleic acids or antigens in a sample using a universal array platform. For example, nucleic acids can be detected by: amplifying at least a portion of a nucleic acid from a sample using a primer pair, the primer pair comprising a first primer and a second primer, the first primer comprising a label and a first oligonucleotide sequence, the first oligonucleotide sequence hybridizing to a first strand of the portion of the nucleic acid, the second primer comprising a second oligonucleotide sequence, the second oligonucleotide sequence hybridizing to a second strand of the portion of the nucleic acid; contacting the amplicons, when present, with a plurality of single-stranded oligonucleotide capture sequences, each attached to a solid support; applying a colloidal detection reagent to the solid support; washing the solid support with a wash solution; and detecting the colloidal detection reagent. The disclosure further relates to specific capture oligonucleotide sequences and tethering oligonucleotide sequences.)

1. A method for detecting a nucleic acid in a sample, the method comprising:

a) amplifying at least a portion of a nucleic acid from a sample using a primer pair under conditions suitable for amplifying an amplicon comprising the portion of the nucleic acid when present in the sample, wherein the primer pair comprises:

1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid, and

2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand and a third oligonucleotide sequence;

b) after step (a), contacting the amplicon, if present, with a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein the amplicon, if present, hybridizes to at least one of the single stranded oligonucleotide capture sequences on its solid support via the third oligonucleotide sequence or a complement of the third oligonucleotide sequence;

c) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal;

d) after (c), washing the solid support with a wash solution; and

e) after steps (a) - (d), detecting the colloidal detection reagent, wherein detection of the colloidal detection reagent on the solid support indicates the presence of the hybridized amplicons, thereby detecting the nucleic acids in the sample.

2. The method of claim 1, wherein the solid support is arranged as a microarray, a multiplex bead array, or a well array.

3. The method of claim 1, wherein the solid support is nitrocellulose, silica, plastic, or hydrogel.

4. The method of claim 1, wherein detecting the colloidal detection reagent in step (e) comprises detecting the colloidal metal.

5. The method of claim 1, wherein detecting the colloidal detection reagent in step (e) comprises:

1) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and

2) detecting the colloidal detection reagent by detecting the formation of the precipitate on a solid support.

6. The method of claim 5, wherein the formation of the precipitate is detected by visual, electronic, or magnetic detection.

7. The method of claim 5 or claim 6, wherein the formation of the precipitate is detected by a mechanical reader.

8. The method of any one of claims 5-7, wherein the developing reagent comprises silver.

9. The method of any one of claims 1-8, wherein the conditions in step (a) are suitable for amplification by Polymerase Chain Reaction (PCR).

10. The method of any one of claims 1-8, wherein the conditions in step (a) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification.

11. The method of any one of claims 1-10, wherein the label comprises biotin and the third oligonucleotide sequence hybridizes to at least one of the single stranded oligonucleotide capture sequences.

12. The method of any one of claims 1-11, wherein each single stranded oligonucleotide capture sequence is coupled to a spacer reagent and the spacer reagent is coupled to a respective solid support.

13. The method of claim 12, wherein the spacer reagent comprises serum albumin.

14. The method of claim 12, wherein the spacer agent comprises a dendrimer.

15. The method of any one of claims 1-14, further comprising washing the solid support with a wash solution after step (b).

16. The method of any one of claims 1-15, wherein the first primer is a forward primer that amplifies in a sense orientation of the nucleic acid and the second primer is a reverse primer that amplifies in an antisense orientation of the nucleic acid.

17. The method of any one of claims 1-15, wherein the second primer is a forward primer that amplifies in a sense orientation of the nucleic acid and the first primer is a reverse primer that amplifies in an antisense orientation of the nucleic acid.

18. The method of any one of claims 1-17, wherein the second primer comprises:

the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and

the third oligonucleotide sequence, wherein the orientation of the third oligonucleotide sequence is in an opposite 5 'to 3' direction compared to the direction of primer extension from the second oligonucleotide sequence.

19. The method of claim 18, wherein the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension.

20. The method of claim 18 or claim 19, wherein the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence.

21. The method of any one of claims 1-17, wherein the portion of the nucleic acid is amplified in step (a) using an excess of the first primer relative to the second primer, and wherein the amplicon, when present, is a single stranded nucleic acid that hybridizes to at least one of the single stranded oligonucleotide capture sequences via the complement of the third oligonucleotide sequence in step (b).

22. The method of claim 21, wherein the portion of the nucleic acid is amplified in step (a) using a ratio of first primer to the second primer of between about 12.5:1 and about 100: 1.

23. The method of any one of claims 1-22, wherein the label of the first primer comprises biotin.

24. The method of claim 23, wherein the first portion of the colloidal detection reagent comprises neutravidin, streptavidin, or an antigen binding domain that specifically binds biotin.

25. The method of claim 24, wherein the first portion of the colloidal detection reagent comprises neutravidin, and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions.

26. The method of any one of claims 1-25, wherein the colloidal detection reagent is applied to the solid support at a final dilution of 0.00001OD to 20OD in step (c).

27. The method of claim 26, wherein the first portion of the colloidal detection reagent comprises neutravidin, wherein the second portion of the colloidal detection reagent comprises colloidal gold ions, and wherein the colloidal detection reagent is applied to the solid support at a final dilution of 0.05OD to 0.2OD in step (c).

28. The method of claim 27, wherein in step (c) 1pL to 1000 μ L of colloidal detection reagent is applied to the solid support per μ L amplicon.

29. The method of any one of claims 1-28, further comprising exposing the sample to a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (a).

30. The method of claim 29, wherein the lysis buffer comprises greater than or equal to 0.5% and less than or equal to 4% N, N-dimethyl-N-dodecylglycine betaine (w/v).

31. The method of claim 29, wherein the lysis buffer comprises greater than or equal to 1% and less than or equal to 2% N, N-dimethyl-N-dodecylglycine betaine (w/v).

32. The method of any one of claims 29-31, wherein the sample is exposed to the lysis buffer at a ratio between 1:50 sample: lysis buffer and 50:1 sample: lysis buffer.

33. The method of claim 32, wherein the portion of the sample is exposed to the lysis buffer at a ratio of about 1:1 sample to lysis buffer.

34. The method of any one of claims 29-33, wherein the lysis buffer further comprises 0.1X to 5X Phosphate Buffered Saline (PBS) buffer or Tris EDTA (TE) buffer.

35. The method of claim 34, wherein the lysis buffer further comprises 1X PBS.

36. The method of any one of claims 1-35, wherein in step (b) the amplicons are hybridized to the solid support in a hybridization buffer comprising 0.1X to 10X sodium citrate saline (SSC) buffer, 0.001% to 30% blocking agent, and 0.01% to 30% crowding agent.

37. The method of claim 36, wherein the blocking agent comprises Bovine Serum Albumin (BSA), polyethylene glycol (PEG), casein, or polyvinyl alcohol (PVA).

38. The method of claim 37, wherein the blocking agent comprises BSA, and the BSA is present at 1% to 3% in the hybridization buffer.

39. The process of any one of claims 36-38, wherein the crowding agent is a polyethylene glycol bisphenol a epichlorohydrin copolymer.

40. The method of claim 39, wherein the polyethylene glycol bisphenol A epichlorohydrin copolymer is present in the hybridization buffer at 1% to 3%.

41. The method of any one of claims 36-40, wherein the hybridization buffer comprises a 2X to 5XSSC buffer.

42. The method of any one of claims 1-41, further comprising blocking the solid support with a solution comprising BSA prior to step (b).

43. The method of claim 41, wherein the solid support is blocked using a 2% BSA solution for 1 hour at 37 ℃.

44. The method of claim 41 or claim 43, further comprising washing the solid support with a wash solution after blocking the solid support.

45. The method of any one of claims 1-44, further comprising washing the solid support with a wash buffer after step (b) and before step (c), the wash buffer comprising 0.1X to 10 XSSC buffer and 0.01% to 30% detergent.

46. The method of claim 45, wherein the detergent comprises 0.05% to 5% N-lauroylsarcosine sodium salt.

47. The method of claim 45 or claim 46, wherein the wash buffer comprises a 1X to 5XSSC buffer.

48. The method of any one of claims 29-47, wherein one or more of the lysis buffer, wash buffer, and hybridization buffer further comprises a control oligonucleotide hybridized to at least one of the single stranded oligonucleotide capture sequences on its solid support.

49. The method of any one of claims 1-48, further comprising, prior to step (a):

(i) contacting the sample with an oligonucleotide coupled to a solid substrate, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample;

(ii) washing the solid substrate under conditions suitable to remove the nucleic acids that have non-specific interactions with the solid substrate but remain hybridized to the oligonucleotides when present in the sample; and

(iii) eluting the nucleic acid when present in the sample from the oligonucleotide, wherein the eluted nucleic acid is subjected to the PCR amplification in step (a).

50. The method of any one of claims 1-48, further comprising, prior to step (a):

(i) contacting the sample with an oligonucleotide, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample,

(ii) (ii) simultaneously with or after step (i), contacting the sample with a solid substrate, wherein the solid substrate is coupled to a first binding moiety, wherein the oligonucleotide is coupled to a second binding moiety that binds to the first binding moiety, and wherein the sample is contacted with the solid substrate under conditions suitable for the second binding moiety to bind to the first binding moiety;

(iii) washing the solid substrate under conditions suitable to remove non-specific interactions with the solid substrate but retain the oligonucleotides and the nucleic acids that hybridize to the oligonucleotides when present in the sample; and

(iv) eluting the nucleic acid when present in the sample from the oligonucleotide, wherein the eluted nucleic acid is subjected to the PCR amplification in step (a).

51. The method of claim 49, wherein the oligonucleotide is coupled to the solid substrate via covalent interactions.

52. The method of claim 49 or claim 50, wherein the oligonucleotide is coupled to the solid substrate via an avidin-biotin or streptavidin-biotin interaction, or wherein the first binding moiety comprises avidin, neutravidin, streptavidin, or a derivative thereof, and the second binding moiety comprises biotin or a derivative thereof.

53. The method of any one of claims 48-52, wherein the solid substrate is positioned in a pipette tip, and wherein step (i) comprises pipetting the sample into the pipette tip.

54. The method of any one of claims 48-53, wherein the solid substrate comprises a matrix or a plurality of beads.

55. The method of any one of claims 1-54, wherein the nucleic acid comprises DNA.

56. The method of any one of claims 1-54, wherein the nucleic acid comprises RNA.

57. The method of claim 56, further comprising incubating at least a portion of the sample with a reverse transcriptase, a primer, and deoxyribonucleotides under conditions suitable for production of cDNA synthesized from the nucleic acids prior to step (a), wherein the portion of the nucleic acids is amplified in step (a) using the cDNA.

58. The method of claim 57, wherein the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the nucleic acid.

59. The method of claim 57 or claim 58, wherein the portion of the sample is incubated with the reverse transcriptase, primer and the deoxyribonucleotides in the presence of an RNase inhibitor.

60. The method of any one of claims 57-59, wherein the portion of the sample is incubated with the reverse transcriptase, primer, and the deoxyribonucleotide in the presence of betaine.

61. The method of claim 60, wherein the betaine is present at a concentration of about 0.2M to about 1.5M.

62. The method of any one of claims 1-61, wherein the nucleic acid comprises viral nucleic acid.

63. The method of claim 62, wherein the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus.

64. The method of any one of claims 1-61, wherein the nucleic acid comprises a bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid.

65. A kit, comprising: a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises a first primer coupled to a label, wherein the first primer hybridizes to a first strand of a nucleic acid; and a second primer, the second primer comprising:

1) a first oligonucleotide sequence that allows primer extension in a 5 'to 3' direction and hybridizes to a second strand of the nucleic acid opposite the first strand;

2) a second oligonucleotide sequence, wherein the orientation of said second oligonucleotide sequence is in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence; and

3) one or more linkers between the 5 'end of the first oligonucleotide sequence and the 5' end of the second oligonucleotide sequence.

66. The kit of claim 65, wherein the second oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension.

67. The kit of claim 65 or claim 66, wherein the label coupled to the first primer comprises biotin.

68. The kit of any one of claims 65-67, further comprising a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein at least one single stranded oligonucleotide sequence hybridizes on its solid support to the second oligonucleotide sequence of a second primer of a primer pair of the plurality of primer pairs.

69. A kit, comprising:

a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and

b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises:

1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid, and

2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each primer pair of the plurality of primer pairs hybridizes to a single-stranded oligonucleotide capture sequence on a solid support thereof.

70. The kit of claim 69, wherein the second oligonucleotide sequence of each primer pair of the plurality of primer pairs allows primer extension in a 5 'to 3' direction, wherein the orientation of the third oligonucleotide sequence of each primer pair of the plurality of primer pairs is in an opposite 5 'to 3' direction compared to the direction of primer extension from the second oligonucleotide sequence, and wherein the second primer of each primer pair of the plurality of primer pairs further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence.

71. The kit of claim 70, wherein the third oligonucleotide sequence of each primer pair of the plurality of primer pairs comprises a modified nucleotide at the 3' terminus that blocks primer extension.

72. The kit of any one of claims 69-71, wherein each of the single stranded oligonucleotide capture sequences is coupled to a spacer reagent on its support, and the spacer reagent is coupled to the solid support.

73. The kit of claim 72, wherein the spacer reagent comprises serum albumin.

74. The kit of claim 72, wherein the spacer reagent comprises a dendrimer.

75. A method for amplifying and detecting a nucleic acid in a sample, the method comprising:

a) incubating at least a portion of the sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair, wherein the primer pair comprises a first primer and a second primer, the first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a portion of the nucleic acid, the second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a first capture moiety;

b) passing the portion of the sample mixed with the amplification mixture through a continuous capillary channel through first, second, and third constant temperature zones under conditions suitable for amplification of an amplicon comprising the portion of the nucleic acid when present in the sample to perform a plurality of cycles, wherein each cycle of the plurality of cycles comprises:

1) passing the portion of the sample mixed with the amplification mixture through the first constant temperature zone via the continuous capillary tubing at a first temperature for a first duration of time, the first temperature and the first duration of time being suitable for denaturing the strands of the nucleic acids present in the sample,

2) after step (b) (1), passing the portion of the sample mixed with the amplification mixture through the second constant temperature zone via the continuous capillary tubing at a second temperature and for a second duration suitable for annealing the first and second primers to corresponding strands of the nucleic acid when present in the sample, and

3) after step (b) (2), passing the portion of the sample mixed with the amplification mixture through the third constant temperature zone via the continuous capillary tubing at a third temperature and for a third duration of time suitable for amplifying the nucleic acid target as present in the sample via the polymerase and primer pair;

c) after the plurality of cycles, associating the amplicons while present in the sample with a first capture moiety attached to a solid support; and

d) detecting association of the amplicon with the solid support when present in the sample, wherein association of the amplicon with the one or more solid supports is indicative of the presence of the nucleic acid in the sample.

76. The method of claim 75, wherein the first capture moiety comprises a third oligonucleotide sequence, and wherein the second capture moiety comprises a single-stranded oligonucleotide capture sequence that hybridizes in step (c) to the third oligonucleotide sequence or to the complement of the third oligonucleotide sequence.

77. The method of claim 75 or claim 76, wherein detecting the association of the amplicon with the solid support, when present, comprises:

i) applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal; and

ii) detecting the colloidal detection reagent.

78. The method of claim 77, wherein detecting the colloidal detection reagent in step (d) (ii) comprises detecting the colloidal metal.

79. The method of claim 77, wherein detecting the colloidal detection reagent in step (d) (ii) comprises:

a) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and

b) detecting the colloidal detection reagent by detecting the formation of the precipitate at the support.

80. The method of claim 79, wherein the formation of a precipitate is detected by visual, electronic, or magnetic detection.

81. The method of claim 79 or claim 80, wherein the formation of a precipitate is detected by a mechanical reader.

82. The method of any one of claims 79-81, wherein the developing reagent comprises silver.

83. The method of any one of claims 77-82, wherein the label comprises biotin or a derivative thereof, and wherein the first portion of the colloidal detection reagent comprises neutravidin, streptavidin, or an antigen binding domain that specifically binds biotin.

84. The method of claim 83, wherein the first portion of the colloidal detection reagent comprises neutravidin and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions.

85. The method of any one of claims 75-84, wherein the conditions in step (b) are suitable for amplification by Polymerase Chain Reaction (PCR).

86. The method of any one of claims 75-84, wherein the conditions in step (b) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification.

87. The method of any one of claims 75-86, wherein the portion of the sample mixed with the PCR amplification mixture is passed through the continuous capillary tubing using a peristaltic pump, a High Performance Liquid Chromatography (HPLC) pump, a precision syringe pump, or a vacuum device.

88. The method of any one of claims 75-87, further comprising, prior to step (b): passing the portion of the sample mixed with the amplification mixture through a pre-heating zone between about 20 ℃ and about 55 ℃ via the continuous capillary tubing.

89. The process of claim 88, wherein the preheating zone is between about 37 ℃ and about 42 ℃.

90. The method of claim 88 or claim 89, wherein the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for up to 30 minutes.

91. The method of claim 90, wherein the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for about 15 minutes.

92. The method of any one of claims 75-91, further comprising, prior to step (b): passing the portion of the sample mixed with the amplification mixture through an activation zone between about 80 ℃ and about 100 ℃ via the continuous capillary tubing.

93. The method of claim 92, wherein the activation zone is between about 90 ℃ and about 95 ℃.

94. The method of claim 92 or claim 93, wherein the portion of the sample mixed with the amplification mixture is passed through the activation zone for up to 20 minutes.

95. The method of claim 94, wherein the portion of the sample mixed with the amplification mixture is passed through the activation region for between about 5 minutes and about 10 minutes.

96. The method of any one of claims 75-95, further comprising, after step (b) and before step (c): passing the portion of the sample mixed with the amplification mixture through an extension zone between about 55 ℃ and about 72 ℃ via the continuous capillary tubing.

97. The method of any one of claims 75-96, further comprising after step (b) and before step (c):

i) mixing at least a portion of a second sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a second primer pair, wherein the second primer pair comprises a third primer and a fourth primer, the third primer comprising a label and a fourth oligonucleotide sequence that hybridizes to a first strand of a portion of a second nucleic acid, the fourth primer comprising a fifth oligonucleotide sequence that hybridizes to a second strand of the portion of the second nucleic acid opposite the first strand, and a third capture moiety;

ii) passing the portion of the second sample mixed with the amplification mixture through the continuous capillary tubing through the first, second, and third constant temperature zones under conditions suitable for amplifying the portion of the second nucleic acid when present in the sample to perform a second plurality of cycles, wherein each cycle of the second plurality of cycles comprises:

1) passing the portion of the second sample mixed with the amplification mixture through the first constant temperature zone via the continuous capillary tubing at the first temperature for the first duration of time, the first temperature and the first duration of time being suitable to denature the strand of the second nucleic acid when present in the second sample,

2) after step (ii) (1), passing the portion of the second sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at the second temperature for the second duration of time, the second temperature and the second duration of time suitable for annealing the third primer and the fourth primer to corresponding strands of the second nucleic acid when present in the second sample, and

3) after step (ii) (2), passing the portion of the second sample mixed with the amplification mixture through the third constant temperature region via the continuous capillary tubing at the third temperature for the third duration of time, the third temperature and the third duration of time suitable for amplifying the second nucleic acid as present in the second sample via the polymerase and second primer pair;

wherein the second nucleic acid, when present in the second sample, is simultaneously associated with the amplified first nucleic acid target, when present in the first sample, with a fourth capture moiety, the fourth capture moiety being associated with the third capture moiety, wherein the fourth capture moiety is coupled to a solid support; and is

Wherein the association of the amplified second nucleic acid with the solid support when present in the second sample is detected simultaneously with hybridization of the amplified first nucleic acid when present in the first sample, and wherein the association of the amplified second nucleic acid target with the solid support is indicative of the presence of the second nucleic acid target in the second sample.

98. The method of claim 97, wherein the first sample and the second sample are the same.

99. The method of claim 97 or claim 98, wherein the first nucleic acid and the second nucleic acid are different.

100. The method of any one of claims 97-99, further comprising, after passing the portion of the first sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the plurality of cycles and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the second plurality of cycles:

passing a sufficient amount of air through the continuous capillary tubing to separate the portion of the first sample mixed with the amplification mixture from the portion of the second sample mixed with the amplification mixture.

101. The method of claim 100, further comprising, after passing the amount of air through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles:

passing a solution comprising sodium hypochlorite at a concentration between about 0.1% and about 10% through the continuous capillary tubing.

102. The method of claim 101, wherein the solution comprises sodium hypochlorite at a concentration of about 1.6%.

103. The method of claim 101 or claim 102, further comprising, after passing the bleach solution through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the second plurality of cycles:

passing a solution comprising thiosulfate in a concentration between about 5mM and about 500mM through the continuous capillary tube.

104. The method of claim 103, wherein the solution comprises thiosulfate in a concentration of about 20 mM.

105. The method of claim 103 or claim 104, further comprising, after passing the thiosulfate solution through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the second plurality of cycles:

passing water through the continuous capillary tubing.

106. The method of claim 105, further comprising, after passing water through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the PCR amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles:

passing a sufficient amount of air through the continuous capillary tubing to separate water from the portion of the second sample mixed with the PCR amplification mixture.

107. The method of any one of claims 75-106, wherein step (a) comprises inserting the portion of the sample into the continuous capillary tubing and mixing the portion of the sample with the amplification mixture using a robotic arm or valve system.

108. The method of any one of claims 75-107, wherein the nucleic acid comprises DNA.

109. The method of any one of claims 75-107, wherein the nucleic acid comprises RNA.

110. The method of claim 109, further comprising, prior to step (a): incubating at least a portion of the sample with a reverse transcriptase, a primer and deoxyribonucleotides under conditions suitable for producing cDNA synthesized from the RNA, wherein the cDNA is mixed with the amplification mixture in step (a).

111. The method of claim 110, wherein the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the RNA.

112. The method of claim 110 or claim 111, wherein the portion of the sample is incubated with the reverse transcriptase, primers, and deoxyribonucleotides while passing through a cDNA synthesis region between about 37 ℃ and about 42 ℃ via the continuous capillary tubing for a time sufficient to produce cDNA synthesized from the RNA.

113. The method of claim 112, further comprising, after passing the portion of the sample mixed with the reverse transcriptase, primer, and deoxyribonucleotides through the cDNA synthesis region and prior to step (b):

passing the portion of the sample mixed with the reverse transcriptase, primer, and deoxyribonucleotide through the continuous capillary tubing through an activation region at about 95 ℃.

114. The method of any one of claims 75-113, wherein, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the first constant temperature zone between about 80 ℃ and about 100 ℃ for 1 second to about 10 minutes.

115. The method of any one of claims 75-114, wherein, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the second constant temperature zone between about 45 ℃ and about 65 ℃ for 2 seconds to about 60 seconds.

116. The method of any one of claims 75-115, wherein, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the third constant temperature zone between about 57 ℃ and about 74 ℃ for 3 seconds to about 60 seconds.

117. The method of any one of claims 75-114, wherein, during each cycle of the plurality of cycles, the portion of the sample mixed with the PCR amplification mixture is passed through both the second constant temperature zone and the third constant temperature zone between about 45 ℃ and about 80 ℃ for between about 0.5 seconds and about 5 minutes.

118. The method of any of claims 75-117, wherein the plurality of cycles comprises greater than or equal to 2 cycles and less than or equal to 100 cycles.

119. The method of any one of claims 75-118, further comprising incubating the portion of the sample with a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (a).

120. The method of any one of claims 75-119, wherein the sample is further mixed with betaine in step (a).

121. The method of any one of claims 75-120, wherein the sample is further mixed with a fluorescent or colored dye in step (a).

122. The method of any one of claims 76-121, wherein the second primer comprises:

the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and

the third oligonucleotide sequence, wherein the orientation of the third oligonucleotide sequence is in an opposite 5 'to 3' direction compared to the direction of primer extension from the second oligonucleotide sequence.

123. The method of claim 122, wherein the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension.

124. The method of claim 122 or claim 123, wherein the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence.

125. The method of any one of claims 75-124, wherein the first capture moiety is attached to a spacer reagent, and wherein the spacer reagent is coupled to the solid support.

126. The method of claim 125, wherein the spacer reagent comprises serum albumin.

127. The method of claim 125, wherein the spacer agent comprises a dendrimer.

128. The method of any one of claims 75-127, wherein the sample comprises a whole blood, serum, saliva, urine, stool, tissue, or environmental sample.

129. The method of any one of claims 75-128, wherein the nucleic acid comprises viral nucleic acid.

130. The method of claim 129, wherein the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus.

131. The method of any one of claims 75-128, wherein the nucleic acid comprises a bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid.

132. An apparatus for amplifying nucleic acid from a sample, the apparatus comprising:

capillary tubing arranged in a plurality of loops around a support, wherein each loop of the plurality of loops comprises a first, a second, and a third constant temperature zone, and wherein the capillary tubing is heated to a first temperature in the first constant temperature zone, a second temperature in the second constant temperature zone, and a third temperature in the third constant temperature zone;

a robotic arm configured to introduce a sample comprising nucleic acids mixed with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair into the capillary tubing; and

a pump or vacuum configured to pass the nucleic acid-containing sample mixed with the amplification mixture through the plurality of loops within the capillary tubing.

133. The apparatus of claim 132, further comprising one or more processors, memory, one or more programs, wherein the one or more programs are stored in the memory and configured to be executed by the one or more processors, the one or more programs including instructions for controlling the temperature of the first, second, and third constant temperature zones.

134. The apparatus of claim 132 or claim 133, the apparatus further comprising:

an incubator for a cDNA synthesis zone, wherein the capillary tubing is heated to between about 37 ℃ and about 42 ℃ upstream of the plurality of loops.

135. The apparatus as set forth in any one of claims 132-134, further comprising:

an incubator for the activation zone, wherein the capillary tubing is heated to about 95 ℃ upstream of the plurality of loops.

136. The apparatus as claimed in any one of claims 132-135, wherein the capillary tube forms a conical, cylindrical or helical shape in each of the plurality of loops.

137. The apparatus as claimed in any one of claims 132-136 wherein the capillary tubing comprises Polytetrafluoroethylene (PTFE).

138. The apparatus of any one of claims 132-137 wherein the plurality of loops of the capillary tube comprises about 25 to about 44 loops.

139. The apparatus of any one of claims 132-138, wherein the robotic arm comprises a peristaltic pump or an HPLC pump configured to introduce the nucleic acid target-containing sample mixed with the amplification mixture into the capillary tube, and wherein the apparatus further comprises a second pump configured to pull the nucleic acid target-containing sample mixed with the amplification mixture through the capillary tube.

140. The apparatus as claimed in any one of claims 132-139, further comprising:

an incubator for a PCR extension zone, wherein the capillary tubing is heated to between about 55 ℃ and about 72 ℃ downstream of the plurality of loops.

141. The apparatus of any one of claims 132-140, wherein the vacuum device configured to pass the nucleic acid-containing sample mixed with the amplification mixture through the plurality of circuits is a peristaltic pump, a High Performance Liquid Chromatography (HPLC) pump, or a precision syringe pump.

142. A method for detecting an antigen in a sample, the method comprising:

a) providing a plurality of single stranded oligonucleotide capture sequences each attached to a solid support;

b) after step (a), contacting the solid support with an antigen binding domain that specifically binds an antigen, wherein the antigen binding domain is coupled to a single stranded oligonucleotide sequence that hybridizes to at least one of the single stranded oligonucleotide capture sequences on the solid support, and wherein the microarray is contacted with an antigen binding domain under conditions suitable for hybridization of the single stranded oligonucleotide sequence of the antigen binding domain to the at least one single stranded oligonucleotide capture sequence on the solid support;

c) after step (a), contacting the solid support with at least a portion of the sample under conditions suitable for the antigen binding domain to bind to the antigen when present in the sample;

d) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that specifically binds to the antigen when present and a second portion that comprises a colloidal metal;

e) after (d), washing the solid support with a wash solution; and

f) after steps (a) - (e), detecting the colloidal detection reagent, wherein detection of the colloidal detection reagent indicates the presence of the antigen in the sample.

143. The method of claim 142, wherein the solid support is arranged as a microarray, a multiplex bead array, or a well array.

144. The method of claim 142, wherein the solid support is nitrocellulose, silica, plastic, or hydrogel.

145. The method of claim 142, wherein detecting the colloidal detection reagent in step (f) comprises detecting the colloidal metal.

146. The method of claim 142, wherein detecting the colloidal detection reagent in step (f) comprises:

1) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and

2) detecting the colloidal detection reagent by detecting the formation of the precipitate.

147. The method of claim 146, wherein the formation of the precipitate is detected by visual, electronic, or magnetic detection.

148. The method of claim 146 or claim 147, wherein the formation of the precipitate is detected by a mechanical reader.

149. The method as recited in any one of claims 146-148, wherein the developing reagent comprises silver.

150. The method of any one of claims 142-149, wherein the first portion comprises a second antigen-binding domain that specifically binds to the antigen, wherein the second antigen-binding domain is coupled to biotin or a derivative thereof, and wherein the colloidal suspension is coupled to avidin, neutravidin, streptavidin, or a derivative thereof that binds to biotin.

151. The method of any one of claims 142-150, wherein the colloidal metal is gold, platinum, palladium, or ruthenium.

152. The method of any one of claims 142-151, wherein the single stranded oligonucleotide capture sequence at each spot of the plurality of spots is coupled to a spacer reagent and the spacer reagent is coupled to the solid support.

153. The method of claim 152, wherein the spacer reagent comprises serum albumin.

154. The method of claim 152, wherein the spacer agent comprises a dendrimer.

155. The method of any one of claims 142-154, further comprising exposing the sample to a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (c).

156. The method of claim 155, wherein the lysis buffer comprises greater than or equal to 0.5% and less than or equal to 4% N, N-dimethyl-N-dodecylglycine betaine (w/v).

157. The method of claim 155, wherein the lysis buffer comprises greater than or equal to 1% and less than or equal to 2% N, N-dimethyl-N-dodecylglycine betaine (w/v).

158. The method as set forth in any one of claims 155-157, wherein the sample is exposed to the lysis buffer at a ratio of 1:50 sample: lysis buffer to 50:1 sample: lysis buffer.

159. The method of claim 158, wherein the portion of the sample is exposed to the lysis buffer at a ratio of about 1:1 sample to lysis buffer.

160. The method of any one of claims 155-159, wherein the lysis buffer further comprises 0.1X to 5X Phosphate Buffered Saline (PBS) buffer or Tris EDTA (TE) buffer.

161. The method of claim 160, wherein the lysis buffer further comprises 1X PBS.

162. The method of any one of claims 142-161, wherein in step (b), the solid support is contacted with the antigen binding domain in the presence of a hybridization buffer comprising 0.1X to 10X sodium citrate saline (SSC) buffer, 0.001% to 30% blocking agent, and 0.01% to 30% crowding agent.

163. The method of claim 162, wherein the blocking agent comprises Bovine Serum Albumin (BSA), polyethylene glycol (PEG), casein, or polyvinyl alcohol (PVA).

164. The method of claim 163, wherein the blocking agent comprises BSA, and the BSA is present at 1% to 3% in the buffer.

165. The method as recited in any one of claims 162-164, wherein the crowding agent is a polyethylene glycol bisphenol a epichlorohydrin copolymer.

166. The method of claim 165, wherein the polyethylene glycol bisphenol a epichlorohydrin copolymer is present in the hybridization buffer at 1% to 3%.

167. The method of any one of claims 162-166, wherein the buffer comprises a 2X to 5X SSC buffer.

168. The method of any one of claims 142-167, further comprising blocking the solid support with a solution comprising BSA prior to steps (b) and (c).

169. The method of claim 168, wherein the solid support is blocked using a 2% BSA solution for 1 hour at 37 ℃.

170. The method of claim 168 or claim 169, further comprising washing the solid support with a wash solution after blocking the solid support.

171. The method of any one of claims 142-170, further comprising washing the solid support with a wash buffer after steps (b) and (c) and before step (d), the wash buffer comprising 0.1X to 10X SSC buffer and 0.01% to 30% detergent.

172. The method of claim 171 wherein the detergent comprises 0.05% to 5% N-lauroylsarcosine sodium salt.

173. The method of claim 171 or claim 172, wherein the wash buffer comprises 1X to 5XSSC buffer.

174. The method of any one of claims 155-173, wherein one or more of the lysis buffer, wash buffer, and hybridization buffer further comprises a control oligonucleotide hybridized to at least one of the single stranded oligonucleotide capture sequences on its solid support.

175. The method of any one of claims 142-174, wherein the antigen is a viral antigen.

176. The method of claim 175, wherein the viral antigen is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus.

177. The method of any one of claims 142-174, wherein the antigen is a bacterial, archaea, protozoan, fungal, plant, or animal antigen.

178. The method of any one of claims 1-177, wherein the sample comprises a whole blood, serum, saliva, urine, stool, tissue, or environmental sample.

179. A kit, comprising:

a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and

b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains specifically binds an antigen, and wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single-stranded oligonucleotide sequence that is substantially complementary to a single-stranded oligonucleotide sequence attached to the solid support.

180. The kit of claim 179, further comprising:

c) a second antigen-binding domain coupled to a colloidal detection reagent, wherein the second antigen-binding domain specifically binds to an antigen that is also specifically bound by an antigen-binding domain of the plurality of antigen-binding domains in (b).

181. A plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from the group consisting of SEQ ID NOS: 1-15.

182. The plurality of sequences of claim 181, wherein the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent and the spacer reagent is coupled to the solid support.

183. The plurality of sequences of claim 182, wherein the spacer agent comprises serum albumin.

184. The plurality of sequences of claim 182, wherein the spacer agent comprises a dendrimer.

185. A kit, comprising:

a) the plurality of sequences of any one of claims 181-184; and

b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOS 16-30.

186. A kit, comprising:

a) the plurality of sequences of any one of claims 181-184; and

b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises:

1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and

2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from the group consisting of SEQ ID NOS: 16-30.

187. A plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from the group consisting of SEQ ID NOS 16-30.

188. The plurality of sequences of claim 187, wherein the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent and the spacer reagent is coupled to the solid support.

189. The plurality of sequences of claim 188, wherein the spacer agent comprises serum albumin.

190. The plurality of sequences of claim 188, wherein the spacer agent comprises a dendrimer.

191. A kit, comprising:

a) the plurality of sequences of any one of claims 187-190; and

b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOs 1-15.

192. A kit, comprising:

a) the plurality of sequences of any one of claims 187-190; and

b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises:

1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and

2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from SEQ ID NOs 1-15.

193. The plurality of sequences of any one of claims 181-184 and 187-190, wherein the solid support is arranged as a microarray, a multiplex bead array, or a well array.

194. The plurality of sequences of any one of claims 181-184 and 187-190, wherein the solid support is nitrocellulose, silica, plastic, or hydrogel.

195. The method of any one of claims 179, 180, 185, 186, 191 and 192, wherein the solid support is arranged as a microarray, a multiplex bead array or a well array.

196. The method of any one of claims 179, 180, 185, 186, 191 and 192, wherein the solid support is nitrocellulose, silica, plastic or hydrogel.

Technical Field

The present disclosure relates to methods and kits for detecting nucleic acids, antigens, or both in a sample using a universal array platform, and to devices for amplifying nucleic acids, and methods of amplifying nucleic acids, comprising at least three constant temperature regions.

Background

Microarray technology has been adapted for the detection of a wide range of nucleic acids, proteins and other antigens, particularly in the field of Nucleic Acid Testing (NAT). Existing microarray formats require printing of different capture reagents (e.g., antibodies or single-stranded oligonucleotides) against the target (usually in duplicate or triplicate), as well as control spots, on an activated slide. When the sample is tested for the presence of the antigen of interest, the sample is reacted with an array, thereby capturing the target, the sample is washed away, the captured target is detected using a labeled antibody, and the reaction is visualized using an amplification/detection method and recorded using a reader. This multi-step process takes time and the cost of printing many different capture spots is greatly increased when testing multiple panels. Furthermore, each array created must be manufactured and quality checked for each target set and each target type (e.g., antibody, antigen, nucleic acid, etc.), requiring the manufacture and inventory of multiple array types, which forces increased costs.

Microarrays are created by attaching capture ligands to a solid surface. As the ability to more accurately spot smaller and smaller spots increases, these microarrays can detect several targets to millions of targets, depending on density, spot size, etc. On a normal array, each spot or series of spots contains a capture oligonucleotide complementary to the target, and an antigen (whereby the antibody in the sample binds to the attached target), or the antibody is printed (attached) on the array to bind to the target in the sample, which is then labeled and detected, although some arrays also utilize unlabeled targets. Since each spot is a different substance and potentially hundreds, thousands or even millions of different capture ligands are required to create a single array, the creation of these arrays becomes very cumbersome and expensive to produce.

Detection of infectious agents, biomarkers, toxins and cells in human clinical samples is crucial for disease-free blood transfusions and transplantations as well as for a variety of diagnostic purposes. However, as described above, the time and cost of manufacturing different microarray slides for different agents, biomarkers, polynucleotides, antigens, etc. may become prohibitive. There is a need for microarray platform technology that allows for robust and accurate detection of multiple nucleic acids or antigens in a sample while reducing associated manufacturing costs.

Disclosure of Invention

To meet these and other needs, a "universal array" approach to microarray platform technology is described herein. Such "microarrays" include any platform capable of performing multiplex assays, including but not limited to planar microarrays, strips, lines, beads, and well arrays. Using this method, a single type of array can be printed, for example, with an array of oligonucleotide spots, each of which is conjugated to a solid support (e.g., via a spacer reagent such as bovine serum albumin BSA). The universal array may be adapted to detect a plurality of nucleic acids in a sample by: amplification is performed using primers with adaptor oligonucleotide sequences that allow hybridization of the resulting PCR products to the oligonucleotide sequences spotted on the array. Each primer pair of nucleic acid sequences of interest may contain one of these unique adaptor sequences, thereby allowing each amplicon to hybridize to a different spot on the array. In this manner, a common or "universal" microarray slide may be adapted to detect a plurality of different nucleic acids. In addition, the universal array method can also be applied to antigens (e.g., polypeptides) using specific antibodies conjugated to adaptor oligonucleotide sequences that hybridize to corresponding oligonucleotide sequences spotted on the array. Thus, manufacturing costs are significantly minimized since a single microarray can be produced and adapted to a variety of different nucleic acid or antigen detection assays.

Accordingly, certain aspects of the present disclosure provide methods for detecting nucleic acids in a sample. In some embodiments, the method comprises: a) amplifying at least a portion of a nucleic acid from a sample using a primer pair under conditions suitable for amplifying an amplicon comprising the portion of the nucleic acid when present in the sample, wherein the primer pair comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid, and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence; b) after step (a), contacting the amplicon, if present, with a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein the amplicon, if present, hybridizes to at least one of the single stranded oligonucleotide capture sequences on its solid support via the third oligonucleotide sequence or a complement of the third oligonucleotide sequence; c) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal; d) after (c), washing the solid support with a wash solution; and e) detecting the colloidal detection reagent after steps (a) - (d), wherein detection of the colloidal detection reagent on the solid support indicates the presence of the hybridized amplicons, thereby detecting the nucleic acids in the sample. In some embodiments, the solid support is arranged as a microarray, a multiplex bead array, or a well array. In some embodiments, the solid support is nitrocellulose, silica, plastic, or hydrogel. In some embodiments, detecting the colloidal detection reagent in step (e) comprises detecting the colloidal metal. In some embodiments, detecting the colloidal detection reagent in step (e) comprises: 1) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and 2) detecting the colloidal detection reagent by detecting the formation of the precipitate on the solid support. In some embodiments, the formation of the precipitate is detected by visual, electronic, or magnetic detection. In some embodiments, the formation of the precipitate is detected by a mechanical reader. In some embodiments, the developing reagent comprises silver. In some embodiments, the conditions in step (a) are suitable for amplification by Polymerase Chain Reaction (PCR). In some embodiments, the conditions in step (a) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification. In some embodiments, the label comprises biotin and the third oligonucleotide sequence hybridizes to at least one of the single stranded oligonucleotide capture sequences. In some embodiments, each single stranded oligonucleotide capture sequence is coupled to a spacer reagent, and the spacer reagent is coupled to a respective solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. In some embodiments, the method further comprises washing the solid support with a wash solution after step (b). In some embodiments, the first primer is a forward primer that amplifies in a sense direction of the nucleic acid and the second primer is a reverse primer that amplifies in an antisense direction of the nucleic acid. In some embodiments, the second primer is a forward primer that amplifies in a sense direction of the nucleic acid and the first primer is a reverse primer that amplifies in an antisense direction of the nucleic acid. In some embodiments, the second primer comprises: the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and said third oligonucleotide sequence, wherein said third oligonucleotide sequence is oriented in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the portion of the nucleic acid is amplified in step (a) using an excess of the first primer relative to the second primer, and wherein the amplicon, when present, is a single-stranded nucleic acid that hybridizes to at least one of the single-stranded oligonucleotide capture sequences in step (b) via the complement of the third oligonucleotide sequence. In some embodiments, the portion of the nucleic acid is amplified in step (a) using a ratio of first primer to the second primer of between about 12.5:1 and about 100: 1. In some embodiments, the label of the first primer comprises biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, streptavidin, or an antigen binding domain that specifically binds biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions. In some embodiments, the colloidal detection reagent is applied to the solid support at a final dilution of 0.00001OD to 20OD in step (c). In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, wherein the second portion of the colloidal detection reagent comprises colloidal gold ions, and wherein in step (c) the colloidal detection reagent is applied to the solid support at a final dilution of 0.05OD to 0.2 OD. In some embodiments, 1pL to 1000 μ L of colloidal detection reagent is applied to the solid support per μ L amplicon in step (c). In some embodiments, the method further comprises exposing the sample to a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (a). In some embodiments, the lysis buffer comprises greater than or equal to 0.5% and less than or equal to 4% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the lysis buffer comprises greater than or equal to 1% and less than or equal to 2% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the sample is exposed to the lysis buffer at a ratio between 1:50 sample: lysis buffer and 50:1 sample: lysis buffer. In some embodiments, the portion of the sample is exposed to the lysis buffer at a ratio of about 1:1 sample to lysis buffer. In some embodiments, the lysis buffer further comprises 0.1X to 5X Phosphate Buffered Saline (PBS) buffer or Tris EDTA (TE) buffer. In some embodiments, the lysis buffer further comprises 1X PBS. In some embodiments, the amplicons are hybridized to the solid support in step (b) in a hybridization buffer comprising 0.1X to 10X sodium citrate saline (SSC) buffer, 0.001% to 30% blocking agent, and 0.01% to 30% crowding agent (crowding agent). In some embodiments, the blocking agent comprises Bovine Serum Albumin (BSA), polyethylene glycol (PEG), casein, or polyvinyl alcohol (PVA). In some embodiments, the blocking agent comprises BSA, and the BSA is present at 1% to 3% in the hybridization buffer. In some embodiments, the crowding agent is a polyethylene glycol bisphenol a epichlorohydrin copolymer. In some embodiments, the polyethylene glycol bisphenol a epichlorohydrin copolymer is present in the hybridization buffer at 1% to 3%. In some embodiments, the hybridization buffer comprises a 2X to 5X SSC buffer. In some embodiments, the method further comprises blocking the solid support with a solution comprising BSA prior to step (b). In some embodiments, the solid support is blocked using a 2% BSA solution for 1 hour at 37 ℃. In some embodiments, the method further comprises washing the solid support with a wash solution after blocking the solid support. In some embodiments, the method further comprises washing the solid support with a wash buffer after step (b) and before step (c), the wash buffer comprising 0.1X to 10X SSC buffer and 0.01% to 30% detergent. In some embodiments, the detergent comprises 0.05% to 5% N-lauroylsarcosine sodium salt. In some embodiments, the wash buffer comprises a 1X to 5X SSC buffer. In some embodiments, one or more of the lysis buffer, wash buffer, and hybridization buffer further comprises a control oligonucleotide hybridized to at least one of the single stranded oligonucleotide capture sequences on its solid support. In some embodiments, the method further comprises, prior to step (a): (i) contacting the sample with an oligonucleotide coupled to a solid substrate, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample; (ii) washing the solid substrate under conditions suitable to remove the nucleic acids that have non-specific interactions with the solid substrate but remain hybridized to the oligonucleotides when present in the sample; and (iii) eluting the nucleic acid from the oligonucleotide when present in the sample, wherein the eluted nucleic acid is subjected to PCR amplification in step (a). In some embodiments, the method further comprises, prior to step (a): (i) contacting the sample with an oligonucleotide, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample, (ii) simultaneously with or after step (i), contacting the sample with a solid substrate, wherein the solid substrate is coupled to a first binding moiety, wherein the oligonucleotide is coupled to a second binding moiety that binds to the first binding moiety, and wherein the sample is contacted with the solid substrate under conditions suitable for the second binding moiety to bind to the first binding moiety; (iii) washing the solid substrate under conditions suitable to remove non-specific interactions with the solid substrate but retain the oligonucleotides and the nucleic acids that hybridize to the oligonucleotides when present in the sample; and (iv) eluting the nucleic acid from the oligonucleotide when present in the sample, wherein the eluted nucleic acid is subjected to PCR amplification in step (a). In some embodiments, the oligonucleotide is coupled to the solid substrate via covalent interactions. In some embodiments, the oligonucleotide is coupled to the solid substrate via an avidin-biotin or streptavidin-biotin interaction, or wherein the first binding moiety comprises avidin, neutravidin, streptavidin, or a derivative thereof, and the second binding moiety comprises biotin or a derivative thereof. In some embodiments, the solid substrate is positioned in a pipette tip, and wherein step (i) comprises pipetting the sample into the pipette tip. In some embodiments, the solid substrate comprises a matrix or a plurality of beads. In some embodiments, the nucleic acid comprises DNA. In some embodiments, the nucleic acid comprises RNA. In some embodiments, the method further comprises incubating at least a portion of the sample with a reverse transcriptase, a primer, and deoxyribonucleotides under conditions suitable for production of cDNA synthesized from the nucleic acid prior to step (a), wherein the portion of the nucleic acid is amplified using the cDNA in step (a). In some embodiments, the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the nucleic acid. In some embodiments, the portion of the sample is incubated with the reverse transcriptase, primer, and the deoxyribonucleotides in the presence of an RNase inhibitor. In some embodiments, the portion of the sample is incubated with the reverse transcriptase, primer, and the deoxyribonucleotide in the presence of betaine. In some embodiments, the betaine is present at a concentration of about 0.2M to about 1.5M. In some embodiments, the nucleic acid comprises viral nucleic acid. In some embodiments, the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments, the nucleic acid comprises bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid.

Other aspects of the disclosure relate to kits or articles of manufacture for detecting nucleic acids in a sample. In some embodiments, the present disclosure relates to a kit comprising: a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises a first primer coupled to a label, wherein the first primer hybridizes to a first strand of a nucleic acid; and a second primer, the second primer comprising: 1) a first oligonucleotide sequence that allows primer extension in a 5 'to 3' direction and hybridizes to a second strand of the nucleic acid opposite the first strand; 2) a second oligonucleotide sequence, wherein the orientation of said second oligonucleotide sequence is in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence; and 3) one or more linkers between the 5 'end of the first oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the second oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the label coupled to the first primer comprises biotin. In some embodiments, the kit further comprises a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein at least one single stranded oligonucleotide sequence hybridizes on its solid support to the second oligonucleotide sequence of the second primer of a primer pair of the plurality of primer pairs. In some embodiments, the present disclosure relates to a kit comprising: a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each primer pair of the plurality of primer pairs hybridizes to a single-stranded oligonucleotide capture sequence on a solid support thereof. In some embodiments, the second oligonucleotide sequence of each primer pair of the plurality of primer pairs allows primer extension in a 5 'to 3' direction, wherein the orientation of the third oligonucleotide sequence of each primer pair of the plurality of primer pairs is in an opposite 5 'to 3' direction compared to the direction of primer extension from the second oligonucleotide sequence, and wherein the second primer of each primer pair of the plurality of primer pairs further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence of each primer pair of the plurality of primer pairs comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, each of the single stranded oligonucleotide capture sequences is coupled to a spacer reagent on its support, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer.

Certain other aspects of the present disclosure relate to methods for amplifying and detecting nucleic acids in a sample. In some embodiments, the method comprises: a) incubating at least a portion of the sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair, wherein the primer pair comprises a first primer and a second primer, the first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a portion of the nucleic acid, the second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a first capture moiety; b) passing the portion of the sample mixed with the amplification mixture through a continuous capillary channel through first, second, and third constant temperature zones under conditions suitable for amplification of an amplicon comprising the portion of the nucleic acid when present in the sample to perform a plurality of cycles, wherein each cycle of the plurality of cycles comprises: 1) passing the portion of the sample mixed with the amplification mixture through the continuous capillary tubing at a first temperature for a first duration of time, the first temperature and the first duration of time being suitable for denaturing the strands of the nucleic acids when present in the sample, 2) after step (b) (1), passing the portion of the sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at a second temperature for a second duration of time, the second temperature and the second duration of time being suitable for annealing the first and second primers to corresponding strands of the nucleic acids when present in the sample, and 3) after step (b) (2), passing the portion of the sample mixed with the amplification mixture through the third constant capillary tubing at a third temperature via the continuous capillary tubing A constant temperature zone and for a third duration of time, the third temperature and the third duration of time suitable for amplifying the nucleic acid target when present in the sample via the polymerase and primer pair; c) after the plurality of cycles, associating the amplicons while present in the sample with a first capture moiety attached to a solid support; and d) detecting the association of the amplicon with the solid support when present in the sample, wherein the association of the amplicon with the one or more solid supports is indicative of the presence of the nucleic acid in the sample. In some embodiments, the first capture moiety comprises a third oligonucleotide sequence, and wherein the second capture moiety comprises a single-stranded oligonucleotide capture sequence that hybridizes to the third oligonucleotide sequence or the complement of the third oligonucleotide sequence in step (c). In some embodiments, detecting the association of the amplicon with the solid support in the presence comprises: i) applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal; and ii) detecting the colloidal detection reagent. In some embodiments, detecting the colloidal detection reagent in step (d) (ii) comprises detecting the colloidal metal. In some embodiments, detecting the colloidal detection reagent in step (d) (ii) comprises: a) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and b) detecting the colloidal detection reagent by detecting the formation of the precipitate at the solid support. In some embodiments, the formation of the precipitate is detected by visual, electronic, or magnetic detection. In some embodiments, the formation of the precipitate is detected by a mechanical reader. In some embodiments, the developing reagent comprises silver. In some embodiments, the label comprises biotin or a derivative thereof, and wherein the first portion of the colloidal detection reagent comprises neutravidin, streptavidin, or an antigen binding domain that specifically binds biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions. In some embodiments, the conditions in step (b) are suitable for amplification by Polymerase Chain Reaction (PCR). In some embodiments, the conditions in step (b) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification. In some embodiments, the portion of the sample mixed with the PCR amplification mixture is passed through the continuous capillary tubing using a peristaltic pump, a High Performance Liquid Chromatography (HPLC) pump, a precision syringe pump, or a vacuum device. In some embodiments, the method further comprises, prior to step (b): passing the portion of the sample mixed with the amplification mixture through a pre-heating zone between about 20 ℃ and about 55 ℃ via the continuous capillary tubing. In some embodiments, the preheating zone is between about 37 ℃ and about 42 ℃. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for up to 30 minutes. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for about 15 minutes. In some embodiments, the method further comprises, prior to step (b): passing the portion of the sample mixed with the amplification mixture through an activation zone between about 80 ℃ and about 100 ℃ via the continuous capillary tubing. In some embodiments, the activation zone is between about 90 ℃ and about 95 ℃. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the activation zone for up to 20 minutes. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the activation zone for between about 5 minutes and about 10 minutes. In some embodiments, the method further comprises after step (b) and before step (c): passing the portion of the sample mixed with the amplification mixture through an extension zone between about 55 ℃ and about 72 ℃ via the continuous capillary tubing. In some embodiments, the method further comprises after step (b) and before step (c): i) mixing at least a portion of a second sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a second primer pair, wherein the second primer pair comprises a third primer and a fourth primer, the third primer comprising a label and a fourth oligonucleotide sequence that hybridizes to a first strand of a portion of a second nucleic acid, the fourth primer comprising a fifth oligonucleotide sequence that hybridizes to a second strand of the portion of the second nucleic acid opposite the first strand, and a third capture moiety; ii) passing the portion of the second sample mixed with the amplification mixture through the continuous capillary tubing through the first, second, and third constant temperature zones under conditions suitable for amplifying the portion of the second nucleic acid when present in the sample to perform a second plurality of cycles, wherein each cycle of the second plurality of cycles comprises: 1) passing the portion of the second sample mixed with the amplification mixture through the first constant temperature region via the continuous capillary tubing at the first temperature for the first duration, the first temperature and the first duration being suitable for denaturing the strand of the second nucleic acid when present in the second sample, 2) after step (ii) (1), passing the portion of the second sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at the second temperature for the second duration, the second temperature and the second duration being suitable for annealing the third primer and the fourth primer to corresponding strands of the second nucleic acid when present in the second sample, and 3) after step (ii) (2), passing the portion of the second sample mixed with the amplification mixture through the third constant temperature region via the continuous capillary tubing at the third temperature for the third duration of time suitable for amplifying the second nucleic acid as present in the second sample via the polymerase and second primer pair; wherein the second nucleic acid, when present in the second sample, is simultaneously associated with the amplified first nucleic acid target, when present in the first sample, with a fourth capture moiety, the fourth capture moiety being associated with the third capture moiety, wherein the fourth capture moiety is coupled to a solid support; and wherein the association of the amplified second nucleic acid with the solid support when present in the second sample is detected simultaneously with hybridization of the amplified first nucleic acid when present in the first sample, and wherein the association of the amplified second nucleic acid target with the solid support is indicative of the presence of the second nucleic acid target in the second sample. In some embodiments, the first sample and the second sample are the same. In some embodiments, the first nucleic acid and the second nucleic acid are different. In some embodiments, the method further comprises, after passing the portion of the first sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the plurality of cycles, and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the second plurality of cycles: passing a sufficient amount of air through the continuous capillary tubing to separate the portion of the first sample mixed with the amplification mixture from the portion of the second sample mixed with the amplification mixture. In some embodiments, the method further comprises, after passing the amount of air through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a solution comprising sodium hypochlorite at a concentration between about 0.1% and about 10% through the continuous capillary tubing. In some embodiments, the solution comprises sodium hypochlorite at a concentration of about 1.6%. In some embodiments, the method further comprises, after passing the bleach solution through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a solution comprising thiosulfate in a concentration between about 5mM and about 500mM through the continuous capillary tube. In some embodiments, the solution comprises thiosulfate at a concentration of about 20 mM. In some embodiments, the method further comprises, after passing the thiosulfate solution through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing water through the continuous capillary tubing. In some embodiments, the method further comprises, after passing water through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the PCR amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a sufficient amount of air through the continuous capillary tubing to separate water from the portion of the second sample mixed with the PCR amplification mixture. In some embodiments, step (a) comprises inserting the portion of the sample into the continuous capillary tubing and mixing the portion of the sample with the amplification mixture using a robotic arm or valve system. In some embodiments, the nucleic acid comprises DNA. In some embodiments, the nucleic acid comprises RNA. In some embodiments, the method further comprises, prior to step (a): incubating at least a portion of the sample with a reverse transcriptase, a primer and deoxyribonucleotides under conditions suitable for producing cDNA synthesized from the RNA, wherein the cDNA is mixed with the amplification mixture in step (a). In some embodiments, the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the RNA. In some embodiments, the portion of the sample is incubated with the reverse transcriptase, primers, and deoxyribonucleotides while passing through a cDNA synthesis region between about 37 ℃ and about 42 ℃ via the continuous capillary tubing for a time sufficient to produce cDNA synthesized from the RNA. In some embodiments, the method further comprises, after passing the portion of the sample mixed with the reverse transcriptase, primer, and deoxyribonucleotides through the cDNA synthesis region and prior to step (b): passing the portion of the sample mixed with the reverse transcriptase, primer, and deoxyribonucleotide through the continuous capillary tubing through an activation region at about 95 ℃. In some embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the first constant temperature zone between about 80 ℃ and about 100 ℃ for 1 second to about 10 minutes. In some embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the second constant temperature zone between about 45 ℃ and about 65 ℃ for 2 seconds to about 60 seconds. In some embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the third constant temperature zone between about 57 ℃ and about 74 ℃ for 3 seconds to about 60 seconds. In some embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the PCR amplification mixture is passed through both the second constant temperature zone and the third constant temperature zone between about 45 ℃ and about 80 ℃ for between about 0.5 seconds and about 5 minutes. In some embodiments, the plurality of cycles comprises greater than or equal to 2 cycles and less than or equal to 100 cycles. In some embodiments, the method further comprises incubating the portion of the sample with a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (a). In some embodiments, the sample is further mixed with betaine in step (a). In some embodiments, the sample is further mixed with a fluorescent or colored dye in step (a). In some embodiments, the second primer comprises: the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and said third oligonucleotide sequence, wherein said third oligonucleotide sequence is oriented in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the first capture moiety is attached to a spacer reagent, and wherein the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. In some embodiments, the sample comprises a whole blood, serum, saliva, urine, stool, tissue, or environmental sample. In some embodiments, the nucleic acid comprises viral nucleic acid. In some embodiments, the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments, the nucleic acid comprises bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid.

Certain other aspects of the present disclosure relate to an apparatus for amplifying nucleic acids from a sample. In some embodiments, the apparatus comprises: capillary tubing arranged in a plurality of loops around a support, wherein each loop of the plurality of loops comprises a first, a second, and a third constant temperature zone, and wherein the capillary tubing is heated to a first temperature in the first constant temperature zone, a second temperature in the second constant temperature zone, and a third temperature in the third constant temperature zone; a robotic arm configured to introduce a sample comprising nucleic acids mixed with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair into the capillary tubing; and a pump or vacuum configured to pass the sample comprising nucleic acids mixed with the amplification mixture through the plurality of loops within the capillary tubing. In some embodiments, the apparatus further comprises one or more processors, memory, one or more programs, wherein the one or more programs are stored in the memory and configured to be executed by the one or more processors, the one or more programs including instructions for controlling the temperature of the first, second, and third constant temperature zones. In some embodiments, the apparatus further comprises an incubator for the cDNA synthesis zone, wherein the capillary tubing is heated to between about 37 ℃ and about 42 ℃ upstream of the plurality of loops. In some embodiments, the apparatus further comprises an incubator for the activation zone, wherein the capillary tubing is heated to about 95 ℃ upstream of the plurality of circuits. In some embodiments, the capillary tubing forms a conical, cylindrical, or helical shape in each of the plurality of loops. In some embodiments, the capillary tubing comprises Polytetrafluoroethylene (PTFE). In some embodiments, the plurality of loops of capillary tubing comprises about 25 to about 44 loops. In some embodiments, the robotic arm comprises a peristaltic pump or an HPLC pump configured to introduce the nucleic acid target-containing sample mixed with an amplification mixture into the capillary tubing, and wherein the apparatus further comprises a second pump configured to pull the nucleic acid target-containing sample mixed with an amplification mixture through the capillary tubing. In some embodiments, the apparatus further comprises an incubator for the PCR extension zone, wherein the capillary tubing is heated to between about 55 ℃ and about 72 ℃ downstream of the plurality of loops. In some embodiments, the vacuum device configured to pass the sample comprising nucleic acids mixed with the amplification mixture through the plurality of circuits is a peristaltic pump, a High Performance Liquid Chromatography (HPLC) pump, or a precision syringe pump.

Certain other aspects of the present disclosure relate to methods for detecting an antigen in a sample. In some embodiments, the method comprises: a) providing a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; b) after step (a), contacting the solid support with an antigen binding domain that specifically binds an antigen, wherein the antigen binding domain is coupled to a single stranded oligonucleotide sequence that hybridizes to at least one of the single stranded oligonucleotide capture sequences on the solid support, and wherein the microarray is contacted with the antigen binding domain under conditions suitable for hybridization of the single stranded oligonucleotide sequence of the antigen binding domain to the at least one single stranded oligonucleotide capture sequence on the solid support; c) after step (a), contacting the solid support with at least a portion of the sample under conditions suitable for the antigen binding domain to bind to the antigen when present in the sample; d) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that specifically binds to the antigen when present and a second portion that comprises a colloidal metal; e) after (d), washing the solid support with a wash solution; and f) detecting the colloidal detection reagent after steps (a) - (e), wherein detection of the colloidal detection reagent indicates the presence of the antigen in the sample. In some embodiments, the solid support is arranged as a microarray, a multiplex bead array, or a well array. In some embodiments, the solid support is nitrocellulose, silica, plastic, or hydrogel. In some embodiments, detecting the colloidal detection reagent in step (f) comprises detecting the colloidal metal. In some embodiments, detecting the colloidal detection reagent in step (f) comprises: 1) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and 2) detecting the colloidal detection reagent by detecting the formation of the precipitate. In some embodiments, the formation of the precipitate is detected by visual, electronic, or magnetic detection. In some embodiments, the formation of the precipitate is detected by a mechanical reader. In some embodiments, the developing reagent comprises silver. In some embodiments, the first portion comprises a second antigen-binding domain that specifically binds to the antigen, wherein the second antigen-binding domain is coupled to biotin or a derivative thereof, and wherein the colloidal suspension is coupled to avidin, neutravidin, streptavidin, or a derivative thereof that binds to biotin. In some embodiments, the colloidal metal is gold, platinum, palladium, or ruthenium. In some embodiments, the single stranded oligonucleotide capture sequence at each spot of the plurality of spots is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. In some embodiments, the method further comprises exposing the sample to a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (c). In some embodiments, the lysis buffer comprises greater than or equal to 0.5% and less than or equal to 4% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the lysis buffer comprises greater than or equal to 1% and less than or equal to 2% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the sample is exposed to the lysis buffer at a ratio between 1:50 sample: lysis buffer and 50:1 sample: lysis buffer. In some embodiments, the portion of the sample is exposed to the lysis buffer at a ratio of about 1:1 sample to lysis buffer. In some embodiments, the lysis buffer further comprises 0.1X to 5X Phosphate Buffered Saline (PBS) buffer or Tris EDTA (TE) buffer. In some embodiments, the lysis buffer further comprises 1X PBS. In some embodiments, in step (b), the solid support is contacted with the antigen binding domain in the presence of a hybridization buffer comprising 0.1X to 10X sodium citrate saline (SSC) buffer, 0.001% to 30% blocking agent, and 0.01% to 30% crowding agent. In some embodiments, the blocking agent comprises Bovine Serum Albumin (BSA), polyethylene glycol (PEG), casein, or polyvinyl alcohol (PVA). In some embodiments, the blocking agent comprises BSA, and the BSA is present at 1% to 3% in the buffer. In some embodiments, the crowding agent is a polyethylene glycol bisphenol a epichlorohydrin copolymer. In some embodiments, the polyethylene glycol bisphenol a epichlorohydrin copolymer is present in the hybridization buffer at 1% to 3%. In some embodiments, the buffer comprises a 2X to 5X SSC buffer. In some embodiments, the method further comprises blocking the solid support with a solution comprising BSA prior to steps (b) and (c). In some embodiments, the solid support is blocked using a 2% BSA solution for 1 hour at 37 ℃. In some embodiments, the method further comprises washing the solid support with a wash solution after blocking the solid support. In some embodiments, the method further comprises washing the solid support with a wash buffer after steps (b) and (c) and before step (d), the wash buffer comprising 0.1X to 10X SSC buffer and 0.01% to 30% detergent. In some embodiments, the detergent comprises 0.05% to 5% N-lauroylsarcosine sodium salt. In some embodiments, the wash buffer comprises a 1X to 5X SSC buffer. In some embodiments, one or more of the lysis buffer, wash buffer, and hybridization buffer further comprises a control oligonucleotide hybridized to at least one of the single stranded oligonucleotide capture sequences on its solid support. In some embodiments, the antigen is a viral antigen. In some embodiments, the viral antigen is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments, the antigen is a bacterial, archaeal, protozoal, fungal, plant, or animal antigen. In some embodiments, the sample comprises a whole blood, serum, saliva, urine, stool, tissue, or environmental sample.

Further provided herein are kits for detecting an antigen in a sample. In some embodiments, the kit comprises: a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains specifically binds an antigen, and wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single-stranded oligonucleotide sequence that is substantially complementary to a single-stranded oligonucleotide sequence attached to the solid support. In some embodiments, the kit further comprises: c) a second antigen-binding domain coupled to a colloidal detection reagent, wherein the second antigen-binding domain specifically binds to an antigen that is also specifically bound by an antigen-binding domain of the plurality of antigen-binding domains in (b).

Further provided herein are a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from SEQ ID NOs 1-15. In some embodiments, the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. Further provided herein is a kit comprising: a) a plurality of single stranded oligonucleotide capture sequences according to any one of the above embodiments; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOS 16-30. Further provided herein is a kit comprising: a) a plurality of single stranded oligonucleotide capture sequences according to any one of the above embodiments; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from SEQ ID NOS 16-30.

Further provided herein are a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from SEQ ID NOs 16-30. In some embodiments, the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. Also provided herein is a kit comprising: a) a plurality of sequences according to any one of the above embodiments; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOs 1-15. Further provided herein is a kit comprising: a) a plurality of sequences according to any one of the above embodiments; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from SEQ ID NOs 1-15.

In some embodiments of any of the various sequences described above, the solid support is arranged as a microarray, a multiplex bead array, or a well array. In some embodiments of any of the various sequences described above, the solid support is nitrocellulose, silica, plastic, or a hydrogel. In some embodiments of any of the kits described above, the solid supports are arranged as a microarray, a multiplex bead array, or a well array. In some embodiments of any of the kits described above, the solid support is nitrocellulose, silica, plastic, or hydrogel.

It should be understood that one, some, or all of the features of the various embodiments described herein may be combined to form further embodiments of the disclosure. These and other aspects of the disclosure will become apparent to those skilled in the art. These and other embodiments of the disclosure are further described by the following detailed description.

Drawings

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the office upon request and payment of the necessary fee.

Figure 1A shows a diagram of a universal array for antigen detection according to some embodiments. BSA: bovine serum albumin.

Figure 1B illustrates detection of biomarkers for hepatitis B (HBsAg) using a universal array, according to some embodiments.

FIG. 2A shows a diagram of amplification primers (tC sequence: SEQ ID NO: 34; HIV target sequence: SEQ ID NO:35) for use in a universal array for Nucleic Acid Testing (NAT), according to some embodiments. FIG. 2B shows a diagram of amplification of a target sequence using the primers shown in FIG. 2A.

Figure 2C shows a diagram of a generic array for Nucleic Acid Testing (NAT), according to some embodiments.

Fig. 2D and 2E illustrate detection of nucleic acids from Hepatitis C Virus (HCV) using a universal array for Nucleic Acid Testing (NAT), according to some embodiments. Reads obtained using samples lacking HCV nucleic acid (fig. 2D) or samples containing HCV nucleic acid (fig. 2E) are shown.

Fig. 3A shows 15 individual probes on a universal array for NAT according to some embodiments.

Fig. 3B shows the effect of different Empigen BB concentrations in sample formulations used with universal arrays for NAT, according to some embodiments.

Fig. 3C illustrates the effect of different hybridization buffer formulations used with a universal array for NAT, according to some embodiments. The indicated buffer formulations are expressed as X/y/z, where X is the strength of the SSC buffer (i.e., "3" indicates 3X SSC buffer), y is the percentage of BSA, and z is the percentage of PEG-C.

Figure 3D illustrates the effect of different NaOH concentrations on elution efficiency for enrichment of nucleic acids of interest from a sample, according to some embodiments.

Figure 3E illustrates the effect of different NaOH concentrations in combination with the amount of enriched nucleic acid of interest used in amplification, according to some embodiments.

Figure 3F illustrates the effect of different elution strategies in combination with the amount of enriched nucleic acid of interest used in amplification, according to some embodiments.

Figure 3G illustrates the effect of different primer concentrations in a nucleic acid enrichment protocol according to some embodiments.

Fig. 4A illustrates enrichment of a nucleic acid of interest from a sample in a pipette tip, according to some embodiments.

Fig. 4B and 4C illustrate the effect of the ratio of biotin-labeled oligonucleotides to neutravidin-labeled colloidal gold, according to some embodiments. The ratio indicated is the biotin-labeled probe-colloidal gold labeled with neutravidin. The dashed rectangles indicate experimental results, and the filled rectangles indicate BSA-gold controls detected via a 2-step assay.

Fig. 5A shows a diagram of a continuous amplification system according to some embodiments.

Fig. 5B and 5C illustrate exemplary embodiments of a continuous amplification system according to some embodiments. Figure 5B shows a robotic arm for obtaining samples, a pump system, an optional pre-heat and activation zone, three constant temperature zones, a waste collection unit, a temperature zone controller, and a power source. Figure 5C shows three zones that can be programmed to provide different temperatures, a temperature control module, optional fan control, power supply, pump module, and optional preheat and activation zones.

Fig. 6A shows a graph for asymmetric amplification of NAT, according to some embodiments.

Fig. 6B shows a ratio of reverse primer to forward primer in asymmetric amplification for NAT according to some embodiments.

Detailed Description

General technique

The techniques and procedures described or cited herein are generally well known to those skilled in the art and are generally employed using conventional methods, such as the widely used methods described in the following references: sambrook et al, Molecular Cloning, A Laboratory Manual 3 rd edition (2001) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; current Protocols in Molecular Biology (edited by F.M. Ausubel et al, (2003)); the series Methods in Enzymology (Academic Press, Inc.: PCR 2: A Practical Approach (M.J. MacPherson, B.D. Hames and G.R. Taylor, eds. (1995)); harlow and Lane editors (1988) Antibodies, A Laboratory Manual, and Animal CellCulture (R.I. Freshney editors (1987)); oligonucleotide Synthesis (m.j. gait editors, 1984); methods in Molecular Biology, human Press; cell Biology A Laboratory Notebook (edited by J.E.Cellis, 1998) Academic Press; animal Cell Culture (r.i. freshney) editions, 1987); introduction to Cell and Tissue Culture (J.P.Mather and P.E.Roberts,1998) Plenum Press; cell and Tissue Culture Laboratory Procedures (A.Doyle, J.B.Griffiths and D.G.Newell editors, 1993-8) J.Wiley and Sons; handbook of experimental Immunology (edited by d.m.weir and c.c.blackwell); gene Transfer vector for Mammalian Cells (edited by j.m.miller and m.p.calos, 1987); PCR The Polymerase Chainreaction (edited by Mullis et al, 1994); current Protocols in Immunology (edited by J.E. Coligan et al, 1991); short Protocols in Molecular Biology (Wiley and Sons, 1999); immunobiology (c.a. janeway and p.travers, 1997); antibodies (p.finch, 1997); antibodies A Practical Approach (D.Catty. eds., IRL Press, 1988-; MonoclonalAntibodies A Practical Approach (edited by P.Shepherd and C.dean, Oxford university Press, 2000); use Antibodies: A Laboratory Manual (E.Harlow and D.Lane (Cold spring harbor Laboratory Press,1999), The Antibodies (M.Zantetti and J.D.Capra eds., Harwood academic Publishers,1995), and Cancer: Principles and Practice of Oncology (V.T.Devita et al eds., J.B.Lippincou Company, 1993).

Microarray

The universal array platform described herein can be used to detect a variety of nucleic acids or antigens of interest.

Nucleic acid detection

Certain aspects of the present disclosure relate to methods for detecting nucleic acids in a sample. In some embodiments, the method comprises: a) amplifying at least a portion of a nucleic acid from a sample using a primer pair under conditions suitable for amplifying an amplicon comprising the portion of the nucleic acid when present in the sample, wherein the primer pair comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid, and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence; b) after step (a), contacting the amplicon, if present, with a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein the amplicon, if present, hybridizes to at least one of the single stranded oligonucleotide capture sequences on its solid support via the third oligonucleotide sequence or a complement of the third oligonucleotide sequence; c) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal; d) after (c), washing the solid support with a wash solution; and e) detecting the colloidal detection reagent after steps (a) - (d), wherein detection of the colloidal detection reagent on the solid support indicates the presence of the hybridized amplicons, thereby detecting the nucleic acids in the sample.

The universal array platform provides an adaptive and universal approach for, for example, diagnostic testing. For example, oligonucleotides of known sequence, 18 bases in length, are covalently attached as small spots to an activated slide or other surface. After binding and blocking excess binding sites, complementary oligonucleotide sequences are covalently attached to an antigen, such as the HIV-1gp41 immunodominant region. If a clinical sample (such as blood) contains antibodies against HIV-1gp41 and is mixed with HIV gp41 peptide labeled with the complementary oligonucleotides, the antibodies bind to the gp41 peptide and, when placed on the microarray described above, the complementary oligonucleotides bind to their ligand partners spotted on the array. Unbound material was washed away and the array probed with biotin-labeled anti-antibody (i.e., monoclonal anti-human Ig or protein a/G). Antibodies that bind gp41 are labeled with gold labeled with an antibiotic molecule (i.e., streptavidin) and gp41 binds to specific spots on the microarray due to the complementary oligonucleotide tether described above. The excess material is washed away and then either the gold-labeled microspots are detected directly, or gold particles are used to catalyze silver deposition (which can be readily detected) to indicate the presence/absence of anti-HIV antibodies against gp41 in the sample, thereby alerting the user to determine whether the person is infected with HIV based on the presence of a detectable amount of anti-HIV-1 gp41 antibodies in the sample.

Importantly, the same oligonucleotide sequences can be used to label different capture reagents, all of which will bind to complementary oligonucleotide sequences on the array. Thus, the next assay can be used to detect HBV, HCV, toxins, hormones, or nucleic acids, all of which can bind to the same spot. The capture reagent will only bind to the same spot based on its oligonucleotide label. Thus, a set of known oligonucleotides can be used to create a universal capture microarray, and the same set of complementary oligonucleotides can be used to label any capture reagent. For example, a 16 × 16 microarray will have 256 spots, each spot having a corresponding oligonucleotide sequence. These oligonucleotide sequences may each be unique, or the array may include redundant spots for confirmation of the results. Assuming each spot is in duplicate, 128 different assays can be distinguished simultaneously. This array can then become a standard universal platform and millions of different targets can be detected by simply labeling different capture reagents with 128 different complementary oligonucleotide sequences, which can be provided as a universal kit. In addition, the same sample may be mixed with different detection solutions containing different tests and/or overlapping tests. For example, a sample may be screened for infectious disease by mixing with solution a, then tested for cancer by mixing another portion of the sample with solution B, then tested for toxins by mixing another portion with solution C, and then tested for nucleic acids against any target of interest by mixing with solution D to detect nucleic acids directly or after an amplification step. The microarray does not change-it remains stationary-but a number of different targets can be tested using different detection solutions. This helps to reduce the cost of manufacturing microarrays and greatly expands their utility for detecting virtually any target. Exemplary features and aspects of the universal array platform are described in more detail below.

As used herein, unless otherwise specified, nucleic acids and/or oligonucleotides broadly refer to polymers of nucleic acids (e.g., DNA or RNA) and are intended to include single-and double-stranded species, as well as species comprising one or more nucleosides/nucleotides that are typically naturally occurring and/or modified (e.g., locked nucleic acids, peptide nucleic acids, PNAs, or the like).

As used herein, unless otherwise specified, "amplicon" refers to the product of any type of nucleic acid amplification described herein, including, but not limited to, Polymerase Chain Reaction (PCR), recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, and loop-mediated isothermal amplification. In some embodiments, the amplicon is a double-stranded nucleic acid. In some embodiments, the amplicon is a single stranded nucleic acid.

As used herein, the term "solid support" refers to any solid or semi-solid structure suitable for attaching biomolecules (e.g., nucleic acids) thereto. The solid support need not be flat or a unitary structure, and can have any type of shape or shapes, including spherical shapes (e.g., beads). The solid support may be arranged in any form. In some embodiments, the solid support is arranged as a microarray (e.g., a flat slide), a multiplex bead array, or a well array. Further, the solid support may be made of any suitable material including, but not limited to, silicon, plastic, glass, polymer, ceramic, photoresist, nitrocellulose, and hydrogel. In some embodiments, the solid support is nitrocellulose, silica, plastic, or hydrogel.

Colloidal suspensions of nanoparticles (e.g., colloidal gold) can be attached to biological probes (e.g., antibodies) and can be used as detection reagents for rapid and sensitive detection in immunostaining. Methods for preparing and using colloidal detection reagents are well known in the art (see, e.g., Hostetler et al, Langmuir 14:17-30,1998; Wang et al, Langmuir 17(19):5739-41, 2001). The colloidal detection reagent may be of any material. In some embodiments, the colloidal detection reagent comprises a metal. Examples of colloidal metals include, but are not limited to, gold (Au), silver (Ag), platinum (Pt), palladium (Pd), copper (Cu), nickel (Ni), ruthenium (Ru), and mixtures thereof. In some embodiments, detecting the colloidal detection reagent in step (e) comprises detecting (e.g., directly detecting) the colloidal metal. In some embodiments, detecting the colloidal detection reagent in step (e) comprises: 1) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and 2) detecting the colloidal detection reagent by detecting the formation of the precipitate on the solid support. In some embodiments, the formation of the precipitate is detected by visual, electronic, or magnetic detection. In some embodiments, the formation of the precipitate is detected by a mechanical reader. In some embodiments described above, the developing reagent comprises silver. In some embodiments described above, silver nitrate and a reducing agent (e.g., hydroquinone) are used. In some embodiments described above, the results of the colloid staining are imaged using a camera (e.g., a CCD camera).

In some embodiments, the conditions in step (a) are suitable for amplification by Polymerase Chain Reaction (PCR). In some embodiments, the conditions in step (a) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification. In some embodiments, the label comprises biotin and the third oligonucleotide sequence hybridizes to at least one of the single stranded oligonucleotide capture sequences.

In some embodiments, each single stranded oligonucleotide capture sequence is coupled to a spacer reagent, and the spacer reagent is coupled to a respective solid support. In some embodiments, the spacer reagent comprises serum albumin (e.g., BSA). In some embodiments, the spacer agent comprises a dendrimer. In some embodiments, the method further comprises washing the solid support with a wash solution after step (b).

In some embodiments, the first primer is a forward primer that amplifies in a sense direction of the nucleic acid and the second primer is a reverse primer that amplifies in an antisense direction of the nucleic acid. In some embodiments, the second primer is a forward primer that amplifies in a sense direction of the nucleic acid and the first primer is a reverse primer that amplifies in an antisense direction of the nucleic acid. In some embodiments, the second primer comprises: the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and said third oligonucleotide sequence, wherein said third oligonucleotide sequence is oriented in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence.

In some embodiments, the label of the first primer comprises biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin or a derivative thereof, streptavidin or a derivative thereof, avidin or a derivative thereof, or an antigen-binding domain (e.g., an antibody or antibody fragment) that specifically binds biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions. In some embodiments, the colloidal detection reagent is applied to the solid support at a final dilution of 0.00001OD to 20OD in step (c). In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, wherein the second portion of the colloidal detection reagent comprises colloidal gold ions, and wherein in step (c) the colloidal detection reagent is applied to the solid support at a final dilution of 0.05OD to 0.2 OD. Various amounts of colloidal detection reagents can be used. In some embodiments, 1pL to 1000 μ L of colloidal detection reagent is applied to the solid support per μ L amplicon in step (c). In some embodiments, 100 μ L of colloidal detection reagent is applied to the solid support in each 1.5 μ L amplicon in step (c).

In some embodiments, the method further comprises exposing the sample to a lysis buffer prior to step (a). In some embodiments, the lysis buffer comprises N, N-dimethyl-N-dodecylglycine betaine. In some embodiments, the lysis buffer comprises greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the lysis buffer comprises greater than or equal to 0.5% and less than or equal to 4% N, N-dimethyl-N-dodecylglycine betaine (w/v). In some embodiments, the lysis buffer comprises greater than or equal to 1% and less than or equal to 2% N, N-dimethyl-N-dodecylglycine betaine (w/v).

In some embodiments, the sample is exposed to the lysis buffer at a ratio between 1:50 sample: lysis buffer and 50:1 sample: lysis buffer. In some embodiments, the portion of the sample is exposed to the lysis buffer at a ratio of about 1:1 sample to lysis buffer. In some embodiments, the lysis buffer further comprises 0.1X to 5X Phosphate Buffered Saline (PBS) buffer or Tris EDTA (TE) buffer. In some embodiments, the lysis buffer further comprises 1X PBS.

In some embodiments, the amplicons are hybridized to the solid support in the presence of a hybridization buffer. Various hybridization buffers are known in the art. In some embodiments, the amplicons are hybridized to the solid support in step (b) in a hybridization buffer comprising 0.1X to 10X sodium citrate saline (SSC) buffer, 0.001% to 30% blocking agent, and 0.01% to 30% crowding agent (crowding agent). In some embodiments, the blocking agent comprises Bovine Serum Albumin (BSA), polyethylene glycol (PEG), casein, or polyvinyl alcohol (PVA). In some embodiments, the blocking agent comprises BSA, and the BSA is present at 1% to 3% in the hybridization buffer. In some embodiments, the crowding agent is a polyethylene glycol bisphenol a epichlorohydrin copolymer. In some embodiments, the polyethylene glycol bisphenol a epichlorohydrin copolymer is present in the hybridization buffer at 1% to 3%. In some embodiments, the hybridization buffer comprises a 2X to 5X SSC buffer.

In some embodiments, the method further comprises blocking the solid support prior to step (b). In some embodiments, the solid support is blocked using a solution comprising BSA. In some embodiments, the solid support is blocked using a 2% BSA solution for 1 hour at 37 ℃. In some embodiments, the method further comprises washing the solid support with a wash solution after blocking the solid support.

In some embodiments, the method further comprises washing the solid support with a wash buffer after step (b) and before step (c). In some embodiments, the wash buffer comprises 0.1X to 10X SSC buffer and 0.01% to 30% detergent. In some embodiments, the detergent comprises 0.05% to 5% N-lauroylsarcosine sodium salt. In some embodiments, the wash buffer comprises a 1X to 5X SSC buffer.

In some embodiments, the method further comprises, prior to step (a): (i) contacting the sample with an oligonucleotide coupled to a solid substrate, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample; (ii) washing the solid substrate under conditions suitable to remove the nucleic acids that have non-specific interactions with the solid substrate but remain hybridized to the oligonucleotides when present in the sample; and (iii) eluting the nucleic acid from the oligonucleotide when present in the sample, wherein the eluted nucleic acid is subjected to PCR amplification in step (a). In some embodiments, the method further comprises, prior to step (a): (i) contacting the sample with an oligonucleotide, wherein the oligonucleotide hybridizes to the nucleic acid when present in the sample, (ii) simultaneously with or after step (i), contacting the sample with a solid substrate, wherein the solid substrate is coupled to a first binding moiety, wherein the oligonucleotide is coupled to a second binding moiety that binds to the first binding moiety, and wherein the sample is contacted with the solid substrate under conditions suitable for the second binding moiety to bind to the first binding moiety; (iii) washing the solid substrate under conditions suitable to remove non-specific interactions with the solid substrate but retain the oligonucleotides and the nucleic acids that hybridize to the oligonucleotides when present in the sample; and (iv) eluting the nucleic acid from the oligonucleotide when present in the sample, wherein the eluted nucleic acid is subjected to PCR amplification in step (a). In some embodiments, the oligonucleotide is coupled to the solid substrate via covalent interactions. In some embodiments, the oligonucleotide is coupled to the solid substrate via an avidin-biotin or streptavidin-biotin interaction, or wherein the first binding moiety comprises avidin, neutravidin, streptavidin, or a derivative thereof, and the second binding moiety comprises biotin or a derivative thereof. In some embodiments, the solid substrate is positioned in a pipette tip, and wherein step (i) comprises pipetting the sample into the pipette tip. In some embodiments, the solid substrate comprises a matrix or a plurality of beads. In some embodiments, the nucleic acid comprises DNA. In some embodiments, the nucleic acid comprises RNA.

In some embodiments, the method further comprises incubating at least a portion of the sample with a reverse transcriptase, a primer, and deoxyribonucleotides under conditions suitable for production of cDNA synthesized from the nucleic acid prior to step (a), wherein the portion of the nucleic acid is amplified using the cDNA in step (a). In some embodiments, the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the nucleic acid. In some embodiments, the portion of the sample is incubated with the reverse transcriptase, primer, and the deoxyribonucleotides in the presence of an RNase inhibitor. In some embodiments, the portion of the sample is incubated with the reverse transcriptase, primer, and the deoxyribonucleotide in the presence of betaine. In some embodiments, the betaine is present at a concentration of about 0.2M to about 1.5M. In some embodiments, the nucleic acid comprises viral nucleic acid. In some embodiments, the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments, the nucleic acid comprises bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid. In some embodiments, the sample comprises whole blood, serum, saliva, urine, stool, tissue, or an environmental sample (e.g., comprising water, soil, etc.).

In some embodiments, any of the reagents described herein (e.g., lysis buffer or hybridization buffer) can comprise a positive control oligonucleotide that hybridizes, for example, to a capture oligonucleotide of the array. Advantageously, this can be used as a positive control to ensure that the correct reagent is used. For example, a variety of capture oligonucleotides may be used to represent different reagents (e.g., lysis buffer, hybridization buffer, etc.), and a particular positive control in each reagent may be used to "encode" the appropriate reagent. When viewed in general terms, the plurality of capture oligonucleotides may indicate that some or all of the steps of microarray preparation/analysis are performed with reagents spiked with one or more positive control oligonucleotides, thereby indicating that the correct reagents are used.

In some embodiments, the present disclosure contemplates adjusting the ratio of the first primer relative to the second primer used in the step of amplifying the nucleic acid in the sample. The ratio of primers can be tilted to preferentially amplify one strand of the nucleic acid over the other-a technique known as asymmetric amplification (see, e.g., McCabe, PCR Protocols: A guido Methods and Applications,76-83,1990). Advantageously, the skewed primer ratio in asymmetric amplification results in a significantly uniform product, which can help increase the intensity of hybridization signals detected on the universal arrays of the present disclosure. In some embodiments of the disclosure, the portion of the nucleic acid is amplified using an excess of the first primer relative to the second primer, and wherein the amplicon, when present, is a single-stranded nucleic acid that hybridizes to at least one of the single-stranded oligonucleotide capture sequences via the complement of the third oligonucleotide sequence. In some embodiments, the portion of the nucleic acid is amplified using a ratio of the first primer to the second primer of between about 12.5:1 and about 100: 1. In some embodiments, the following ratio of the first primer to the second primer is used: at least about 2:1, at least about 5:1, at least about 10:1, at least about 15:1, at least about 20:1, at least about 25:1, at least about 30:1, at least about 35:1, at least about 40:1, at least about 45:1, at least about 50:1, at least about 55:1, at least about 60:1, at least about 65:1, at least about 70:1, at least about 75:1, at least about 80:1, at least about 85:1, at least about 90:1, at least about 95:1, at least about 100:1, at least about 150:1, or at least about 200: 1.

Antigen detection

In addition to nucleic acids, the universal array platform described herein can be used to detect a variety of antigens of interest. Accordingly, some aspects of the present disclosure relate to methods for detecting an antigen in a sample. In some embodiments, the method comprises: a) providing a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; b) after step (a), contacting the solid support with an antigen binding domain that specifically binds an antigen, wherein the antigen binding domain is coupled to a single stranded oligonucleotide sequence that hybridizes to at least one of the single stranded oligonucleotide capture sequences on the solid support, and wherein the microarray is contacted with the antigen binding domain under conditions suitable for hybridization of the single stranded oligonucleotide sequence of the antigen binding domain to the at least one single stranded oligonucleotide capture sequence on the solid support; c) after step (a), contacting the solid support with at least a portion of the sample under conditions suitable for the antigen binding domain to bind to the antigen when present in the sample; d) after step (a), applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that specifically binds to the antigen when present and a second portion that comprises a colloidal metal; e) after (d), washing the solid support with a wash solution; and f) detecting the colloidal detection reagent after steps (a) - (e), wherein detection of the colloidal detection reagent indicates the presence of the antigen in the sample.

In some embodiments, the antigen comprises a polypeptide, a lipid, or a carbohydrate. In certain embodiments, the antigen is a polypeptide antigen.

Any of the compositions and methods described above with respect to nucleic acid detection may also be used for antigen detection, including, but not limited to, solid supports, colloidal detection reagents and detection methods thereof, visualization reagents, spacer reagents, lysis buffers, blocking agents, crowding agents, hybridization buffers, and wash buffers.

In some embodiments, the first portion comprises a second antigen-binding domain that specifically binds to the antigen, wherein the second antigen-binding domain is coupled to biotin or a derivative thereof, and wherein the colloidal suspension is coupled to avidin, neutravidin, streptavidin, or a derivative thereof that binds to biotin. In some embodiments, the colloidal metal is gold, platinum, palladium, or ruthenium. In some embodiments, the single stranded oligonucleotide capture sequence at each spot of the plurality of spots is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. In some embodiments, the method further comprises exposing the sample to a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (c). In some embodiments, the antigen is a viral antigen. In some embodiments, the viral antigen is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments, the antigen is a bacterial, archaeal, protozoal, fungal, plant, or animal antigen. In some embodiments, the sample comprises whole blood, serum, saliva, urine, stool, tissue, or an environmental sample (e.g., comprising water, soil, etc.).

Device for measuring the position of a moving object

Other aspects of the disclosure relate to a device or apparatus for amplifying nucleic acids in a sample. In some embodiments, the apparatus or device comprises: capillary tubing arranged in a plurality of loops around a support, wherein each loop of the plurality of loops comprises a first, a second, and a third constant temperature zone, and wherein the capillary tubing is heated to a first temperature in the first constant temperature zone, a second temperature in the second constant temperature zone, and a third temperature in the third constant temperature zone; a robotic arm configured to introduce a sample comprising nucleic acids mixed with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair into the capillary tubing; and a pump or vacuum configured to pass the sample comprising nucleic acids mixed with the amplification mixture through the plurality of loops within the capillary tubing.

To detect nucleic acids in a sample using the methods described herein, amplification of at least a portion of the nucleic acids can be used to hybridize to an array. Thus, in some aspects, the present disclosure contemplates devices that can be used to amplify nucleic acids of interest. In some embodiments, the present disclosure relates to an apparatus for nucleic acid amplification having a capillary tube, a robotic arm, and a pump or vacuum device.

The amplification of the nucleic acid is performed in the capillary tubing. The capillary tubing is arranged in a plurality of loops around a support, wherein each loop in the plurality of loops comprises a first, a second, and a third constant temperature zone, and wherein the capillary tubing is heated to a first temperature in the first constant temperature zone, a second temperature in the second constant temperature zone, and a third temperature in the third constant temperature zone. Each of these regions may correspond to a portion of a standard PCR or other amplification reaction, i.e., denaturation, annealing, and extension of the PCR. For isothermal amplification, each zone may be heated to the same temperature (e.g., 37 ℃). Advantageously, the capillary tubing allows for an increased heat transfer rate, which means that the target reaction temperature can be achieved quickly and the reaction time can be shortened. The capillary tubing in each of the plurality of loops may be formed in any shape, such as, but not limited to, a conical shape, a cylindrical shape, or a helical shape. The capillary tubing may comprise any material, such as, but not limited to, Polytetrafluoroethylene (PTFE). The plurality of loops of the capillary tubing may include any number of loops, such as, but not limited to, about 25 to about 44 loops (e.g., corresponding to the number of amplification cycles).

The pump or vacuum of the apparatus may be configured to pass the nucleic acid-containing sample mixed with the amplification mixture through the plurality of loops within the capillary tubing. A variety of pumps and vacuum devices well known in the art may be used with the apparatus. In some embodiments, the pump or vacuum device is a peristaltic pump. In some embodiments, the pump or vacuum device is a High Performance Liquid Chromatography (HPLC) pump. In some embodiments, the pump or vacuum device is a precision syringe pump.

The robotic arm of the apparatus may be configured to introduce a sample comprising nucleic acids mixed with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair into the capillary tubing. In some embodiments, the robotic arm comprises a peristaltic pump or an HPLC pump configured to introduce the nucleic acid target-containing sample mixed with an amplification mixture into the capillary tubing, and wherein the apparatus further comprises a second pump configured to pull the nucleic acid target-containing sample mixed with an amplification mixture through the capillary tubing.

Additional components may be added to the device. In some embodiments, the apparatus further contains one or more processors, memory, one or more programs, wherein the one or more programs are stored in the memory and configured to be executed by the one or more processors, the one or more programs including instructions for controlling the temperature of the first, second, and third constant temperature zones. In some embodiments, the apparatus further comprises an incubator for the cDNA synthesis zone (e.g., when the sample is RNA), wherein the capillary tubing is heated to between about 37 ℃ to about 42 ℃ upstream of the plurality of loops. In some embodiments, the incubator is a temperature bath, a Peltier device, or a resistance heater. In some embodiments, the sample mixed with the amplification mixture is maintained in the cDNA synthesis region for 15 seconds to 30 minutes. In some embodiments, the apparatus further comprises an incubator for the activation zone, wherein the capillary tubing is heated to about 95 ℃ upstream of the plurality of circuits. In some embodiments, the apparatus further contains an incubator for the PCR extension zone, wherein the capillary tubing is heated to between about 55 ℃ and about 72 ℃ downstream of the plurality of loops.

The pumps, robotic arms, and various temperature zones may all be controlled by a system control panel, allowing for modifications to each component, e.g., the temperature of the different zones may be changed. In addition, the control panel can be used to vary the pumping rate, thereby altering the length of time spent in each temperature zone of the main amplification zone. Thus, in some embodiments, the apparatus may further include one or more processors, memory, one or more programs, wherein the one or more programs are stored in the memory and configured to be executed by the one or more processors, the one or more programs including instructions for controlling the temperature of the first, second, and third constant temperature zones.

The temperature of the capillary tubing may be maintained at a desired temperature in different temperature zones according to standard techniques known in the art. In some embodiments, the temperature of one or more temperature zones is maintained by a peltier or resistive heater. In some embodiments, polyimide tape (e.g., inside copper tubing) is used to isolate one or more temperature zones.

In some embodiments, after the circuit is completed, the amplicons are applied to a microarray (e.g., a solid support of the present disclosure) using a robotic arm. In some embodiments, a dye is added, for example, to help visualize the liquid spotted on the microarray. In some embodiments, after completing the loop, the amplicons are collected into a container with hybridization buffer and then added to the microarray (e.g., manually by pipetting, or using a robotic arm).

The apparatus described above may be used in any of the methods of the present disclosure. For example, in some embodiments, the method comprises: a) incubating at least a portion of the sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair, wherein the primer pair comprises a first primer and a second primer, the first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a portion of the nucleic acid, the second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a first capture moiety; b) passing the portion of the sample mixed with the amplification mixture through a continuous capillary channel through first, second, and third constant temperature zones under conditions suitable for amplification of an amplicon comprising the portion of the nucleic acid when present in the sample to perform a plurality of cycles, wherein each cycle of the plurality of cycles comprises: 1) passing the portion of the sample mixed with the amplification mixture through the continuous capillary tubing at a first temperature for a first duration of time, the first temperature and the first duration of time being suitable for denaturing the strands of the nucleic acids when present in the sample, 2) after step (b) (1), passing the portion of the sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at a second temperature for a second duration of time, the second temperature and the second duration of time being suitable for annealing the first and second primers to corresponding strands of the nucleic acids when present in the sample, and 3) after step (b) (2), passing the portion of the sample mixed with the amplification mixture through the third constant capillary tubing at a third temperature via the continuous capillary tubing A constant temperature zone and for a third duration of time, the third temperature and the third duration of time suitable for amplifying the nucleic acid target when present in the sample via the polymerase and primer pair; c) after the plurality of cycles, associating the amplicons while present in the sample with a first capture moiety attached to a solid support; and d) detecting the association of the amplicon with the solid support when present in the sample, wherein the association of the amplicon with the one or more solid supports is indicative of the presence of the nucleic acid in the sample.

The general procedures for amplifying and detecting nucleic acids in a sample using the above-described apparatus are described below, and any of the reagents or techniques described above may be employed.

The method can include incubating at least a portion of the sample in an initial vessel with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a primer pair, wherein the primer pair comprises a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a portion of the nucleic acid and a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a first capture moiety.

Then, using a pump and a robotic arm to pass the portion of the sample mixed with the amplification mixture through a continuous capillary conduit through first, second, and third constant temperature zones under conditions suitable for amplification of an amplicon comprising the portion of the nucleic acid when present in the sample to perform a plurality of cycles, wherein each cycle of the plurality of cycles comprises: 1) passing the portion of the sample mixed with the amplification mixture through the continuous capillary tubing at a first temperature for a first duration of time, the first temperature and the first duration of time being suitable for denaturing the strands of the nucleic acids when present in the sample, 2) after step (b) (1), passing the portion of the sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at a second temperature for a second duration of time, the second temperature and the second duration of time being suitable for annealing the first and second primers to corresponding strands of the nucleic acids when present in the sample, and 3) after step (b) (2), passing the portion of the sample mixed with the amplification mixture through the third constant capillary tubing at a third temperature via the continuous capillary tubing A constant temperature zone and for a third duration of time, the third temperature and the third duration of time suitable for amplifying the nucleic acid target when present in the sample via the polymerase and primer pair.

Next, after the plurality of cycles, the amplicons, as present in the sample, can be associated with a first capture moiety attached to a solid support.

Finally, the association of the amplicon with the solid support when present in the sample can be detected, wherein the association of the amplicon with the one or more solid supports is indicative of the presence of the nucleic acid in the sample.

In some embodiments, the first capture moiety comprises a third oligonucleotide sequence, and wherein the second capture moiety comprises a single-stranded oligonucleotide capture sequence that hybridizes to the third oligonucleotide sequence or the complement of the third oligonucleotide sequence in step (c). In some embodiments, detecting the association of the amplicon with the solid support in the presence comprises: i) applying a colloidal detection reagent to the solid support, wherein the colloidal detection reagent comprises a first portion that binds to the label of the amplicon when present and a second portion that comprises a colloidal metal; and ii) detecting the colloidal detection reagent. In some embodiments, detecting the colloidal detection reagent in step (d) (ii) comprises detecting the colloidal metal. In some embodiments, detecting the colloidal detection reagent in step (d) (ii) comprises: a) applying a developing reagent to the solid support, wherein the developing reagent is adapted to form a precipitate in the presence of the colloidal metal; and b) detecting the colloidal detection reagent by detecting the formation of the precipitate at the solid support. In some embodiments, the formation of the precipitate is detected by visual, electronic, or magnetic detection. In some embodiments, the formation of the precipitate is detected by a mechanical reader. In some embodiments, the developing reagent comprises silver. In some embodiments, the label comprises biotin or a derivative thereof, and wherein the first portion of the colloidal detection reagent comprises neutravidin, streptavidin, or an antigen binding domain that specifically binds biotin. In some embodiments, the first portion of the colloidal detection reagent comprises neutravidin, and wherein the second portion of the colloidal detection reagent comprises colloidal gold ions. In some embodiments, the conditions in step (b) are suitable for amplification by Polymerase Chain Reaction (PCR). In some embodiments, the conditions in step (b) are suitable for amplification by: recombinase-polymerase assay (RPA), nucleic acid sequencing-based strand assay (NASBA), rolling circle amplification, branched chain amplification, ligation amplification, or loop-mediated isothermal amplification. In some embodiments, the portion of the sample mixed with the PCR amplification mixture is passed through the continuous capillary tubing using a peristaltic pump, a High Performance Liquid Chromatography (HPLC) pump, a precision syringe pump, or a vacuum device. In some embodiments described above, the method may further comprise, prior to step (b): passing the portion of the sample mixed with the amplification mixture through a pre-heating zone between about 20 ℃ and about 55 ℃ via the continuous capillary tubing. In some embodiments, the preheating zone is between about 37 ℃ and about 42 ℃. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for up to 30 minutes. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the pre-heating zone for about 15 minutes. In some embodiments described above, the method may further comprise, prior to step (b): passing the portion of the sample mixed with the amplification mixture through an activation zone between about 80 ℃ and about 100 ℃ via the continuous capillary tubing. In some embodiments, the activation zone is between about 90 ℃ and about 95 ℃. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the activation zone for up to 20 minutes. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the activation zone for between about 5 minutes and about 10 minutes. In some embodiments described above, the method may further comprise after step (b) and before step (c): passing the portion of the sample mixed with the amplification mixture through an extension zone between about 55 ℃ and about 72 ℃ via the continuous capillary tubing. In some of the above embodiments, the method may further comprise after step (b) and before step (c): i) mixing at least a portion of a second sample with an amplification mixture comprising deoxyribonucleotides, a polymerase, and a second primer pair, wherein the second primer pair comprises a third primer and a fourth primer, the third primer comprising a label and a fourth oligonucleotide sequence that hybridizes to a first strand of a portion of a second nucleic acid, the fourth primer comprising a fifth oligonucleotide sequence that hybridizes to a second strand of the portion of the second nucleic acid opposite the first strand, and a third capture moiety; ii) passing the portion of the second sample mixed with the amplification mixture through the continuous capillary tubing through the first, second, and third constant temperature zones under conditions suitable for amplifying the portion of the second nucleic acid when present in the sample to perform a second plurality of cycles, wherein each cycle of the second plurality of cycles comprises: 1) passing the portion of the second sample mixed with the amplification mixture through the first constant temperature region via the continuous capillary tubing at the first temperature for the first duration, the first temperature and the first duration being suitable for denaturing the strand of the second nucleic acid when present in the second sample, 2) after step (ii) (1), passing the portion of the second sample mixed with the amplification mixture through the second constant temperature region via the continuous capillary tubing at the second temperature for the second duration, the second temperature and the second duration being suitable for annealing the third primer and the fourth primer to corresponding strands of the second nucleic acid when present in the second sample, and 3) after step (ii) (2), passing the portion of the second sample mixed with the amplification mixture through the third constant temperature region via the continuous capillary tubing at the third temperature for the third duration of time suitable for amplifying the second nucleic acid as present in the second sample via the polymerase and second primer pair; wherein the second nucleic acid, when present in the second sample, is simultaneously associated with the amplified first nucleic acid target, when present in the first sample, with a fourth capture moiety, the fourth capture moiety being associated with the third capture moiety, wherein the fourth capture moiety is coupled to a solid support; and wherein the association of the amplified second nucleic acid with the solid support when present in the second sample is detected simultaneously with hybridization of the amplified first nucleic acid when present in the first sample, and wherein the association of the amplified second nucleic acid target with the solid support is indicative of the presence of the second nucleic acid target in the second sample.

In some embodiments, the first sample and the second sample may or may not be the same. In some embodiments, the first sample and the second sample are the same. In some embodiments, the first sample and the second sample are different samples. In some embodiments, the first nucleic acid and the second nucleic acid may or may not be the same. In some embodiments, the first nucleic acid and the second nucleic acid are the same. In some embodiments, the first nucleic acid and the second nucleic acid are different. It should be noted that the same nucleic acid from different samples can be detected using the devices and methods described herein.

In some embodiments described above, the method can further comprise, after passing the portion of the first sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the plurality of cycles, and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones for the second plurality of cycles: passing a sufficient amount of air through the continuous capillary tubing to separate the portion of the first sample mixed with the amplification mixture from the portion of the second sample mixed with the amplification mixture. In some embodiments, the method may further comprise, after passing the amount of air through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a solution comprising sodium hypochlorite at a concentration between about 0.1% and about 10% through the continuous capillary tubing. In some embodiments, the solution comprises sodium hypochlorite at a concentration of about 1.6%. In some embodiments, the method may further comprise, after passing the bleach solution through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a solution comprising thiosulfate in a concentration between about 5mM and about 500mM through the continuous capillary tube. In some embodiments, the solution comprises thiosulfate at a concentration of about 20 mM. In some embodiments, the method may further comprise, after passing the thiosulfate solution through the continuous capillary tubing and before passing the portion of the second sample mixed with the amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing water through the continuous capillary tubing. In some embodiments, the method may further comprise, after passing water through the continuous capillary tubing and prior to passing the portion of the second sample mixed with the PCR amplification mixture through the first, second, and third constant temperature zones to perform the second plurality of cycles: passing a sufficient amount of air through the continuous capillary tubing to separate water from the portion of the second sample mixed with the PCR amplification mixture. In some embodiments, the water and air pass through protocol comprises four water pulses of 20 seconds each between samples, separated by air pulses of 20 seconds. In some embodiments that may be combined with any of the preceding embodiments, step (a) comprises inserting the portion of the sample into the continuous capillary tubing and mixing the portion of the sample with the amplification mixture using a robotic arm or valve system.

In some embodiments that may be combined with any of the preceding embodiments, the nucleic acid comprises DNA. In some embodiments that may be combined with any of the preceding embodiments, the nucleic acid comprises RNA. In some embodiments, the method may further comprise, prior to step (a): incubating at least a portion of the sample with a reverse transcriptase, a primer and deoxyribonucleotides under conditions suitable for producing cDNA synthesized from the RNA, wherein the cDNA is mixed with the amplification mixture in step (a). In some embodiments, the primer used prior to step (a) is a random primer, a poly-dT primer, or a primer specific for the portion of the RNA. In some embodiments, wherein the portion of the sample is incubated with the reverse transcriptase, primers, and deoxyribonucleotides while passing through a cDNA synthesis region between about 37 ℃ and about 42 ℃ via the continuous capillary tubing for a time sufficient to produce cDNA synthesized from the RNA. In some embodiments, the method may further comprise, after passing the portion of the sample mixed with the reverse transcriptase, primer and deoxyribonucleotides through the cDNA synthesis region and prior to step (b): passing the portion of the sample mixed with the reverse transcriptase, primer, and deoxyribonucleotide through the continuous capillary tubing through an activation region at about 95 ℃. In some embodiments that may be combined with any of the preceding embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the first constant temperature zone between about 80 ℃ and about 100 ℃ for 1 second to about 10 minutes. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the first constant temperature zone between about 90 ℃ and about 97 ℃ for 2 seconds to about 20 seconds. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the first constant temperature zone at about 95 ℃ for at least 10 seconds. In some embodiments that may be combined with any of the preceding embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the second constant temperature zone between about 45 ℃ and about 65 ℃ for 2 seconds to about 60 seconds. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the second constant temperature zone at about 55 ℃ for at least 15 seconds. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the second constant temperature zone between about 50 ℃ and about 57 ℃ for 2 seconds to about 60 seconds. In some embodiments that may be combined with any of the preceding embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the amplification mixture is passed through the third constant temperature zone between about 57 ℃ and about 74 ℃ for 3 seconds to about 60 seconds. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the third constant temperature zone between about 65 ℃ and about 72 ℃ for 3 seconds to about 60 seconds. In some embodiments, the portion of the sample mixed with the amplification mixture is passed through the third constant temperature zone between about 65 ℃ and about 72 ℃ for at least 15 seconds. In some embodiments, if isothermal or LAMP amplification is used, all three constant temperature regions may have the same temperature, e.g., 37 ℃. Furthermore, the speed of the pump or vacuum device can be controlled for all constant temperature zones to alter the length of time the sample mixed with the amplification mixture spends in each constant temperature zone.

In some embodiments that may be combined with any of the preceding embodiments, during each cycle of the plurality of cycles, the portion of the sample mixed with the PCR amplification mixture is passed through both the second and third constant temperature zones between about 45 ℃ and about 80 ℃ for between about 0.5 seconds and about 5 minutes. In some embodiments that may be combined with any of the preceding embodiments, the plurality of cycles comprises greater than or equal to 2 cycles and less than or equal to 100 cycles. In some embodiments that may be combined with any of the preceding embodiments, the method may further comprise incubating the portion of the sample with a lysis buffer comprising greater than or equal to 0.1% and less than or equal to 10% N, N-dimethyl-N-dodecylglycine betaine (w/v) prior to step (a). In some embodiments that may be combined with any of the preceding embodiments, the sample is further mixed with betaine in step (a). In some embodiments that may be combined with any of the preceding embodiments, the sample is further mixed with a fluorescent or colored dye in step (a). In some embodiments that may be combined with any of the preceding embodiments, the second primer comprises: the second oligonucleotide sequence, wherein the second oligonucleotide sequence allows primer extension in the 5 'to 3' direction; and said third oligonucleotide sequence, wherein said third oligonucleotide sequence is oriented in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the second primer further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments that may be combined with any of the preceding embodiments, the first capture moiety is attached to a spacer reagent, and wherein the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. In some embodiments that may be combined with any of the preceding embodiments, the sample comprises a whole blood, serum, saliva, urine, stool, tissue, or environmental sample. In some embodiments that may be combined with any of the preceding embodiments, the nucleic acid comprises a viral nucleic acid. In some embodiments, the viral nucleic acid is from a virus selected from the group consisting of: HIV, HBV, HCV, West Nile virus, Zika virus, and parvovirus. In some embodiments that may be combined with any of the preceding embodiments, the nucleic acid comprises a bacterial, archaea, protozoan, fungal, plant, or animal nucleic acid. In some embodiments, the sample comprises whole blood, serum, saliva, urine, stool, tissue, or an environmental sample (e.g., comprising water, soil, etc.).

Kits and articles of manufacture

Other aspects of the disclosure relate to kits or articles of manufacture for detecting a nucleic acid or antigen in a sample.

In some embodiments, the present disclosure relates to a kit having: a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises a first primer coupled to a label, wherein the first primer hybridizes to a first strand of a nucleic acid; and a second primer, the second primer comprising: 1) a first oligonucleotide sequence that allows primer extension in a 5 'to 3' direction and hybridizes to a second strand of the nucleic acid opposite the first strand; 2) a second oligonucleotide sequence, wherein the orientation of said second oligonucleotide sequence is in an opposite 5 'to 3' direction compared to the direction of primer extension from said second oligonucleotide sequence; and 3) one or more linkers between the 5 'end of the first oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the second oligonucleotide sequence comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments, the label coupled to the first primer comprises biotin. In some embodiments described above, the kit may further comprise a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, and wherein at least one single stranded oligonucleotide sequence hybridizes on its solid support to the second oligonucleotide sequence of the second primer of a primer pair of the plurality of primer pairs.

In some embodiments, the present disclosure relates to a kit having: a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of the portion of the nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each primer pair of the plurality of primer pairs hybridizes to a single-stranded oligonucleotide capture sequence on a solid support thereof. In some embodiments, the second oligonucleotide sequence of each primer pair of the plurality of primer pairs allows primer extension in a 5 'to 3' direction, wherein the orientation of the third oligonucleotide sequence of each primer pair of the plurality of primer pairs is in an opposite 5 'to 3' direction compared to the direction of primer extension from the second oligonucleotide sequence, and wherein the second primer of each primer pair of the plurality of primer pairs further comprises one or more linkers between the 5 'end of the third oligonucleotide sequence and the 5' end of the second oligonucleotide sequence. In some embodiments, the third oligonucleotide sequence of each primer pair of the plurality of primer pairs comprises a modified nucleotide at the 3' terminus that blocks primer extension. In some embodiments described above, each of the single stranded oligonucleotide capture sequences is coupled to a spacer reagent on its support, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer reagent comprises a dendrimer.

In some embodiments, the present disclosure relates to a kit having: a) a plurality of single stranded oligonucleotide capture sequences each attached to a solid support; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains specifically binds an antigen, and wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single-stranded oligonucleotide sequence that is substantially complementary to a single-stranded oligonucleotide sequence attached to the solid support. In some embodiments, the kit further comprises: c) a second antigen-binding domain coupled to a colloidal detection reagent, wherein the second antigen-binding domain specifically binds to an antigen that is also specifically bound by an antigen-binding domain of the plurality of antigen-binding domains in (b).

In some embodiments, the kits of the present disclosure further comprise a primer sequence. For example, for the detection of HBV, the kit of the present disclosure may further comprise an amplification primer for detecting HBV nucleic acid (e.g., HBV sAg). In some embodiments, an amplicon comprising sequence TTC CTA GGA CCC CTG CTC GTG TTA CAG GCG GGGTTT TTC TTG TTG ACA AGA ATC CTC ACA ATA CCG CAG AGT CTA GAC TCG TGG TGG ACTTCT CTC AAT TTT CTA GGG GG (SEQ ID NO:33) is amplified. In some embodiments, the amplification primers comprise: a first primer comprising sequence CCC CCT AGA AAA TTG AGA GAA GTC CAC CAC G (SEQ ID NO:32) and a second primer comprising sequence ATT CCT AGG ACC CCT GCT CGT GTT A (SEQ ID NO: 31). In some embodiments, the first primer comprises biotin coupled to the 5' end.

Oligonucleotides

Other aspects of the disclosure relate to single stranded oligonucleotides, such as tethers or capture sequences. These sequences may be used interchangeably as tethering or capturing sequences. For example, provided herein are a plurality of single stranded oligonucleotide capture sequences, wherein each sequence of the plurality of single stranded oligonucleotide capture sequences is independently selected from SEQ ID NOs 1-15. In addition, provided herein are a plurality of single stranded oligonucleotide capture sequences, wherein each sequence of the plurality of single stranded oligonucleotide capture sequences is independently selected from SEQ ID NOs 16-30. Advantageously, these sequences have been identified from thousands of potential sequences for robust and consistent hybridization, lack of secondary structure, and absence of homology to naturally occurring sequences (e.g., associated with the human genome).

Further provided herein are a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from SEQ ID NOs 1-15. In some embodiments, the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer agent comprises a dendrimer. Further provided herein is a kit having: a) a plurality of single stranded oligonucleotide capture sequences according to any one of the above embodiments; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOS 16-30. Further provided herein is a kit having: a) a plurality of single stranded oligonucleotide capture sequences according to any one of the above embodiments; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from SEQ ID NOS 16-30.

Further provided herein are a plurality of single stranded oligonucleotide capture sequences each attached to a solid support, wherein each single stranded oligonucleotide capture sequence is independently selected from SEQ ID NOs 16-30. In some embodiments, the single stranded oligonucleotide capture sequence at each solid support is coupled to a spacer reagent, and the spacer reagent is coupled to the solid support. In some embodiments, the spacer reagent comprises serum albumin. In some embodiments, the spacer reagent comprises a dendrimer. Further provided herein is a kit having: a plurality of sequences according to any one of the above embodiments; and b) a plurality of antigen binding domains, wherein each antigen binding domain of the plurality of antigen binding domains is coupled to a single stranded oligonucleotide sequence independently selected from SEQ ID NOs 1-15. Further provided herein is a kit having: a) a plurality of sequences according to any one of the above embodiments; and b) a plurality of primer pairs, wherein each primer pair of the plurality of primer pairs comprises: 1) a first primer comprising a label and a first oligonucleotide sequence that hybridizes to a first strand of a nucleic acid; and 2) a second primer comprising a second oligonucleotide sequence that hybridizes to a second strand of the portion of the nucleic acid opposite the first strand, and a third oligonucleotide sequence, wherein the third oligonucleotide sequence of each first primer is independently selected from SEQ ID NOs 1-15.

In some embodiments that may be combined with any of the preceding embodiments, the solid support is arranged as a microarray, a multiplex bead array, or a well array. In some embodiments that may be combined with any of the preceding embodiments, the solid support is nitrocellulose, silica, plastic, or a hydrogel. In some embodiments that may be combined with any of the preceding embodiments, the solid support is arranged as a microarray, a multiplex bead array, or a well array. In some embodiments that may be combined with any of the preceding embodiments, the solid support is nitrocellulose, silica, plastic, or a hydrogel.

The disclosure will be more fully understood by reference to the following examples. However, they should not be construed as limiting any aspect or scope of the disclosure in any way.