System and method for information storage and retrieval using flow cells

文档序号：704498 发布日期：2021-04-13 浏览：26次中文

阅读说明：本技术 使用流动池进行信息存储和检索的系统和方法 (System and method for information storage and retrieval using flow cells ) 是由吴怡萱 A·基亚 T·库拉纳 A·阿甘 A·卡鲁纳卡兰陈锡君于 2020-05-26 设计创作，主要内容包括：一种方法包括将寡核苷酸嫁接至流动池中并制备多核苷酸文库。每个多核苷酸已被写成包含可检索信息,并包含与嫁接至流动池的测序起始引物之一互补的区域。索引每个多核苷酸以允许对所述核苷酸和相对于所述文库中的其他多核苷酸其所包含的信息进行离散识别。另一种方法包括将包含具有反向互补连接序列的两个序列的两个多核苷酸写至流动池上。延伸所述多核苷酸中的一个以产生第三多核苷酸,所述第三多核苷酸包含作为第一序列和第二序列的组合的序列。用第四序列的第三连接序列写入第四多核苷酸。第三连接序列是包含第三序列的第三多核苷酸的一部分的反向互补序列,并在第三多核苷酸和第四多核苷酸之间形成第二连接桥。(One method includes grafting oligonucleotides into a flow cell and preparing a polynucleotide library. Each polynucleotide has been written to contain retrievable information and to contain a region complementary to one of the sequencing initiation primers grafted to the flow cell. Each polynucleotide is indexed to allow discrete identification of the nucleotide and the information it contains relative to the other polynucleotides in the library. Another method includes writing two polynucleotides comprising two sequences with reverse complementary joining sequences onto a flow cell. Extending one of the polynucleotides to produce a third polynucleotide comprising a sequence that is a combination of the first sequence and the second sequence. Writing a fourth polynucleotide with a third linker sequence of the fourth sequence. The third connecting sequence is the reverse complement of a portion of the third polynucleotide comprising the third sequence and forms a second connecting bridge between the third polynucleotide and the fourth polynucleotide.)

1. A method, comprising:

grafting a plurality of oligonucleotides to the flow cell, wherein each oligonucleotide is a first sequencing initiation primer or a second sequencing initiation primer;

preparing a polynucleotide library comprising polynucleotide sequences, wherein each polynucleotide sequence has been written to comprise specific retrievable information, and wherein each polynucleotide sequence comprises a region complementary to one of the sequencing initiation primers grafted to the flow cell;

binding a library of polynucleotide sequences to the sequencing initiation primer grafted to the flow cell;

indexing or barcoding each polynucleotide sequence in a manner that allows discrete identification of the polynucleotide sequence and the information it contains relative to other polynucleotide sequences in the library; and

the information contained in the library of polynucleotide sequences is retrieved by identifying and referencing the particular index or barcode associated with the sequence of interest.

2. The method of claim 1, further comprising locating each polynucleotide in the polynucleotide library on the flow cell in a spatially predetermined manner or in a random manner.

3. The method of any one or more of claims 1-2, further comprising writing sequence information on and reading sequence information from the same flow cell.

4. The method of any one or more of claims 1-3, further comprising indexing or barcoding the polynucleotides prior to binding the polynucleotides to the flow cell or after binding the polynucleotides to the flow cell.

5. The method of any one or more of claims 1-4, further comprising creating the index and the barcode to comprise a plurality of predetermined sequences of adenine, thymine, cytosine, and guanine, alone or in various combinations with each other.

6. The method of any one or more of claims 1-5, further comprising adding a molecule or nanoparticle to each polynucleotide to create an optical or digital signature that can only be decrypted with a known key.

7. The method of any one or more of claims 1-6, further comprising using P5/P7 as the first and second initiation primers and P6/P8 as the third and fourth initiation primers.

8. A method, comprising:

grafting a plurality of oligonucleotides to a flow cell already adapted for sequencing-by-synthesis, wherein each oligonucleotide is a member of a first sequencing initiation primer and a second sequencing initiation primer pair or a third sequencing initiation primer and a fourth sequencing initiation primer pair;

binding a library of polynucleotide sequences to the sequence initiating primers grafted to the flow cell;

the information contained in the library of polynucleotide sequences is retrieved by identifying and referencing the particular index or barcode associated with the sequence of interest.

9. The method of claim 8, further comprising locating each sequence in the polynucleotide library on the flow cell in a spatially predetermined manner or in a random manner.

10. The method of any one or more of claims 8-9, further comprising writing sequence information on and reading sequence information from the same flow cell.

11. The method of any one or more of claims 8-10, further comprising indexing or barcoding the polynucleotides prior to binding the polynucleotides to the flow cell or after binding the polynucleotides to the flow cell.

12. The method of any one or more of claims 8-11, further comprising creating indices and barcodes to comprise a plurality of predetermined sequences of adenine, thymine, cytosine, and guanine, alone or in various combinations with each other.

13. The method of any one or more of claims 8-12, further comprising adding molecules or nanoparticles to each polynucleotide sequence to create an optical signature or digital DNA signature that can only be decrypted with a known key.

14. The method of any one or more of claims 8-13, wherein the flow cell comprises reaction wells and interstitial spaces between the reaction wells.

15. The method of claim 14, further comprising using P5/P7 as a first starting primer pair and P6/P8 as a second starting primer pair, wherein a P5/P7 pair is grafted to the reaction well, and wherein a P6/P8 pair is grafted to the interstitial space.

16. A method, comprising:

binding a library of polynucleotide sequences to the sequencing initiation primer grafted to the flow cell;

amplifying the polynucleotide sequence using sequencing-by-synthesis; and

the information contained in the library of polynucleotide sequences is retrieved by identifying and referencing the particular index or barcode associated with the various sequences of interest.

17. The method of claim 16, further comprising locating each sequence in the polynucleotide library on the flow cell in a spatially predetermined manner or in a random manner.

18. The method of any one or more of claims 16-17, further comprising creating the index and the barcode to comprise a plurality of predetermined sequences of adenine, thymine, cytosine, and guanine, alone or in various combinations with each other.

19. The method of any one or more of claims 16-18, further comprising adding molecules or nanoparticles to each polynucleotide to create an optical signature or digital DNA signature that can only be decrypted with a known key.

20. The method of any one or more of claims 16-19, wherein the flow cell comprises reaction wells and interstitial spaces located between the reaction wells, and further comprising using P5/P7 as a first starting primer pair and P6/P8 as a second starting primer pair, wherein a P5/P7 pair is grafted to the reaction wells, and wherein a P6/P8 pair is grafted to the interstitial spaces.

21. A method, comprising:

writing a second polynucleotide comprising a second DNA sequence onto the flow cell at a second predetermined position, wherein the second polynucleotide comprises a second linker sequence of the second DNA sequence, wherein the second linker sequence is the reverse complement of the first linker sequence, and wherein the first linker sequence and the second linker sequence form a first linker bridge between the first polynucleotide and the second polynucleotide;

extending at least one of the first and second polynucleotides based on the ligated first and second polynucleotides to produce a third polynucleotide comprising a third DNA sequence that is a combination of the first and second DNA sequences;

writing a fourth polynucleotide comprising a fourth DNA sequence onto the flow cell at a third predetermined position, wherein the fourth polynucleotide comprises a third linker sequence of the fourth DNA sequence, wherein the third linker sequence is the reverse complement of at least a portion of the third polynucleotide comprising the third DNA sequence, and forms a second connecting bridge between the third polynucleotide and the fourth polynucleotide; and

extending at least one of the third and fourth polynucleotides based on the ligated third and fourth polynucleotides to produce a fifth polynucleotide comprising a fifth DNA sequence that is a combination of the first, second, and third DNA sequences.

22. The method of claim 21, further comprising providing a calibration tool on the flow cell to provide quality assurance regarding sequence integrity of extended sequences produced by the method.

23. The method of any one or more of claims 21-22, wherein the flow cell is suitable for sequencing-by-synthesis.

24. The method of any one or more of claims 21-23, wherein the first primer comprises a first primer nucleotide sequence and the second primer comprises a second primer nucleotide sequence, the first primer nucleotide sequence differing from the second primer nucleotide sequence by at least one nucleotide.

25. The method of any one or more of claims 21-24, wherein the first linking sequence is a first homopolymer and wherein the second linking sequence is a second homopolymer that is reverse complementary to the first homopolymer.

26. The method of any one or more of claims 21 to 24, wherein the first and second junction sequences are the reverse complement components of a gene.

27. The method of any one or more of claims 21-26, wherein the fifth polynucleotide has at least 2000 base pairs (bp).

28. The method of any one or more of claims 21-27, wherein the first predetermined distance is at least 100 nm.

29. A method, comprising:

writing a first polynucleotide comprising a first DNA sequence onto a flow cell at a first predetermined position, wherein the first polynucleotide comprises a first linker sequence of the first DNA sequence, and wherein the flow cell is suitable for sequencing-by-synthesis;

30. The method of claim 21, further comprising providing a calibration tool on the flow cell to provide quality assurance as to the sequence integrity of the extended sequence generated by the method.

31. The method of any one or more of claims 29-30, wherein the first primer comprises a first primer nucleotide sequence and the second primer comprises a second primer nucleotide sequence, the first primer nucleotide sequence differing from the second primer nucleotide sequence by at least one nucleotide.

32. The method of any one or more of claims 29-31, wherein the first linking sequence is a first homopolymer and wherein the second linking sequence is a second homopolymer that is reverse complementary to the first homopolymer.

33. The method of any one or more of claims 29-31, wherein the first and second connecting sequences are complementary components of a gene of interest being prepared using the method.

34. The method of any one or more of claims 29-33, wherein the distance between the predetermined locations is at least 100 nm.

35. The method of any one or more of claims 29-34, wherein the first and second junction sequences are the reverse complement components of a gene.

36. A method, comprising:

writing a first polynucleotide comprising a first DNA sequence onto a flow cell at a first predetermined location, wherein the first polynucleotide comprises a first linker sequence of the first DNA sequence, wherein the flow cell is suitable for sequencing by synthesis, wherein the flow cell comprises a plurality of individual pixels, and wherein the first predetermined location represents a first pixel;

writing a second polynucleotide comprising a second DNA sequence onto the flow cell at a second predetermined location, wherein the second polynucleotide comprises a second junction sequence of the second DNA sequence, wherein the second junction sequence is the reverse complement of the first junction sequence, wherein the first junction sequence and the second junction sequence form a first junction bridge between the first polynucleotide and the second polynucleotide, wherein the flow cell is suitable for sequencing by synthesis, wherein the flow cell comprises a plurality of individual pixels, and wherein the second predetermined location represents a second pixel;

extending at least one of the first polynucleotide and the second polynucleotide based on the ligated first polynucleotide and the second polynucleotide to produce a third polynucleotide comprising a third DNA sequence that is a combination of the first DNA sequence and the second DNA sequence;

37. The method of claim 36, further comprising providing a calibration tool on the flow cell to provide quality assurance as to the sequence integrity of the extended sequence generated by the method.

38. The method of any one or more of claims 36-37, wherein the first primer comprises a first primer nucleotide sequence and the second primer comprises a second primer nucleotide sequence, the first primer nucleotide sequence differing from the second primer nucleotide sequence by at least one nucleotide.

39. The method of any one or more of claims 36-38, wherein the first linking sequence is a first homopolymer and wherein the second linking sequence is a second homopolymer that is reverse complementary to the first homopolymer.

40. The method of any one or more of claims 36-38, wherein the first and second connecting sequences are complementary components of a gene of interest being prepared using the method, and wherein the distance between the pixels is at least 100 nm.

Background

Computer systems have used a variety of different mechanisms to store data, including magnetic storage, optical storage, and solid state storage. Such forms of data storage may have disadvantages in the form of read and write speed, duration of data retention, power usage, or data density.

Just as naturally occurring DNA can be read, machine-written DNA can also be read. Pre-existing DNA reading techniques may include array-based cycle sequencing assays (e.g., sequencing-by-synthesis (SBS)), in which dense arrays of DNA features (e.g., template nucleic acids) are sequenced by iterative cycles of enzymatic manipulation. After each cycle, an image may be captured and then analyzed with other images to determine a sequence of machine-written DNA features. In another biochemical assay, an unknown analyte having an identifiable label (e.g., a fluorescent label) can be exposed to an array of known probes having predetermined addresses within the array. Observing the chemical reaction that occurs between the probe and the unknown analyte can help identify or reveal the identity of the analyte.

Disclosure of Invention

Systems and methods for information storage and retrieval using SBS flow cells are described herein.

According to one embodiment, a first method for storing and retrieving information from a flow cell is provided. The method comprises grafting a plurality of oligonucleotides to a flow cell, wherein each oligonucleotide is a first sequencing initiation primer or a second sequencing initiation primer. The method further comprises preparing a polynucleotide library comprising polynucleotide sequences, wherein each polynucleotide sequence has been written to comprise specific retrievable information, and wherein each polynucleotide sequence comprises a region complementary to one of the sequencing initiation primers grafted to the flow cell. The method further comprises binding the library of polynucleotide sequences to the sequencing initiation primer grafted to the flow cell. The method further comprises indexing or barcoding each polynucleotide sequence in a manner that allows discrete identification of the polynucleotide sequence and the information it contains relative to other polynucleotide sequences in the library. The method further comprises retrieving information contained in the library of polynucleotide sequences by identifying and referencing a particular index or barcode associated with the sequence of interest.

There are variations of any one or more of the above embodiments, wherein the method further comprises locating each polynucleotide in the library of polynucleotides on the flow cell in a spatially predetermined manner or in a random manner.

There are variations of any one or more of the above embodiments, wherein the method further comprises writing sequence information on and reading sequence information from the same flow cell.

There is a variation of any one or more of the embodiments above, wherein the method further comprises indexing or barcoding the polynucleotides prior to binding the polynucleotides to the flow cell or after binding the polynucleotides to the flow cell.

There is a variation of any one or more of the embodiments above, wherein the method further comprises creating the index and the barcode to comprise a plurality of predetermined sequences of adenine, thymine, cytosine, and guanine, alone or in various combinations with each other.

There are variations of any one or more of the above embodiments, wherein the method further comprises adding a molecule or nanoparticle to each polynucleotide to create an optical or digital signature that can only be decrypted with a known key.

There is a variation of any one or more of the embodiments above, wherein the method further comprises using P5/P7 as the first and second initiation primers and P6/P8 as the third and fourth initiation primers.

According to another embodiment, another method for storing and retrieving information from a flow cell is provided. The method comprises grafting a plurality of oligonucleotides to a flow cell already suitable for sequencing by synthesis, wherein each oligonucleotide is a member of a first sequencing initiation primer and a second sequencing initiation primer pair or a third sequencing initiation primer and a fourth sequencing initiation primer pair. The method further comprises preparing a polynucleotide library comprising polynucleotide sequences, wherein each polynucleotide sequence has been written to comprise specific retrievable information, and wherein each polynucleotide sequence comprises a region complementary to one of the starting primers grafted to the flow cell. The method further comprises binding a library of polynucleotide sequences to the sequence initiation primers grafted to the flow cell. The method further comprises indexing or barcoding each polynucleotide sequence in a manner that allows discrete identification of the polynucleotide sequence and the information it contains relative to other polynucleotide sequences in the library. The method further comprises retrieving information contained in the library of polynucleotide sequences by identifying and referencing a particular index or barcode associated with the sequence of interest.

There are variations of any one or more of the above embodiments, wherein the method further comprises locating each sequence in the polynucleotide library on the flow cell in a spatially predetermined manner or in a random manner.

There are variations of any one or more of the above embodiments, wherein the method further comprises writing sequence information on and reading sequence information from the same flow cell.

There are variations of any one or more of the above embodiments, wherein the method further comprises creating the index and barcode to comprise a plurality of predetermined sequences of adenine, thymine, cytosine, and guanine, alone or in various combinations with each other.

There are variations of any one or more of the above embodiments, wherein the method further comprises adding a molecule or nanoparticle to each polynucleotide sequence to create an optical signature or digital DNA signature that can only be decrypted with a known key.

There are variations of any one or more of the above embodiments, wherein the flow cell comprises reaction wells and interstitial spaces between the reaction wells.

There is a variation of any one or more of the embodiments above, wherein the method further comprises using P5/P7 as a first starting primer pair and P6/P8 as a second starting primer pair, wherein a P5/P7 pair is grafted to the reaction well, and wherein a P6/P8 pair is grafted to the interstitial space.

In yet another embodiment, another method for storing and retrieving information from a flow cell is provided. The method comprises grafting a plurality of oligonucleotides to a flow cell already suitable for sequencing by synthesis, wherein each oligonucleotide is a member of a first sequencing initiation primer and a second sequencing initiation primer pair or a third sequencing initiation primer and a fourth sequencing initiation primer pair. The method further comprises preparing a polynucleotide library comprising polynucleotide sequences, wherein each polynucleotide sequence has been written to comprise specific retrievable information, and wherein each polynucleotide sequence comprises a region complementary to one of the sequencing initiation primers grafted to the flow cell. The method further comprises binding a library of polynucleotide sequences to the sequencing initiation primer grafted to the flow cell. The method further comprises indexing or barcoding each polynucleotide sequence in a manner that allows discrete identification of the polynucleotide sequence and the information it contains relative to other polynucleotide sequences in the library. The method further comprises amplifying the polynucleotide sequence using sequencing-by-synthesis. The method further comprises retrieving information contained in the library of polynucleotide sequences by identifying and referencing specific indices or barcodes associated with a plurality of sequences of interest.

There are variations of any one or more of the above embodiments, wherein the method further comprises adding a molecule or nanoparticle to each polynucleotide to create an optical signature or digital DNA signature that can only be decrypted with a known key.

There is a variation of any one or more of the above embodiments, wherein the flow cell comprises reaction wells and interstitial spaces between the reaction wells, and further comprising using P5/P7 as a first starting primer pair and P6/P8 as a second starting primer pair, wherein a P5/P7 pair is grafted to the reaction wells, and wherein a P6/P8 pair is grafted to the interstitial spaces.

According to another embodiment, another method of producing a polynucleotide is provided. The method includes writing a first polynucleotide comprising a first DNA sequence onto a flow cell at a first predetermined location, wherein the first polynucleotide comprises a first linker sequence of the first DNA sequence. The method further comprises writing a second polynucleotide comprising a second DNA sequence onto the flow cell at a second predetermined location, wherein the second polynucleotide comprises a second linker sequence of the second DNA sequence, wherein the second linker sequence is the reverse complement of the first linker sequence, and wherein the first linker sequence and the second linker sequence form a first linker bridge between the first polynucleotide and the second polynucleotide. The method further includes extending at least one of the first polynucleotide and the second polynucleotide based on the ligated first polynucleotide and second polynucleotide to produce a third polynucleotide comprising a third DNA sequence that is a combination of the first DNA sequence and the second DNA sequence. The method further comprises writing a fourth polynucleotide comprising a fourth DNA sequence onto the flow cell at a third predetermined position, wherein the fourth polynucleotide comprises a third linker sequence of the fourth DNA sequence, wherein the third linker sequence is the reverse complement of at least a portion of the third polynucleotide comprising the third DNA sequence, and a second connecting bridge is formed between the third polynucleotide and the fourth polynucleotide. The method further includes extending at least one of a third polynucleotide and a fourth polynucleotide based on the ligated third polynucleotide and fourth polynucleotide to produce a fifth polynucleotide comprising a fifth DNA sequence that is a combination of the first DNA sequence, the second DNA sequence, and the third DNA sequence.

There are variations of any one or more of the above embodiments, wherein the method further comprises providing a calibration tool on the flow cell to provide quality assurance as to the sequence integrity of the extended sequence produced by the method.

There are variations of any one or more of the above embodiments, wherein the flow cell is adapted for sequencing-by-synthesis.

There is a variation of any one or more of the embodiments above, wherein the first primer comprises a first primer nucleotide sequence and the second primer comprises a second primer nucleotide sequence, the first primer nucleotide sequence differing from the second primer nucleotide sequence by at least one nucleotide.

There are variations of any one or more of the above embodiments, wherein the first linking sequence is a first homopolymer and wherein the second linking sequence is a second homopolymer reverse complementary to the first homopolymer.

There are variations of any one or more of the above embodiments, wherein the first and second joining sequences are the reverse complement components of a gene.

There is a variation of any one or more of the embodiments above, wherein the fifth polynucleotide has at least 2000 base pairs (bp).

There are variations of any one or more of the above embodiments, wherein the first predetermined distance is at least 100 nm.

According to another embodiment, another method for producing a polynucleotide is provided. The method comprises writing a first polynucleotide comprising a first DNA sequence onto a flow cell at a first predetermined position, wherein the first polynucleotide comprises a first linker sequence of the first DNA sequence, and wherein the flow cell is suitable for sequencing-by-synthesis. The method further comprises writing a second polynucleotide comprising a second DNA sequence onto the flow cell at a second predetermined location, wherein the second polynucleotide comprises a second linker sequence of the second DNA sequence, wherein the second linker sequence is the reverse complement of the first linker sequence, and wherein the first linker sequence and the second linker sequence form a first linker bridge between the first polynucleotide and the second polynucleotide. The method further includes extending at least one of the first polynucleotide and the second polynucleotide based on the ligated first polynucleotide and second polynucleotide to produce a third polynucleotide comprising a third DNA sequence that is a combination of the first DNA sequence and the second DNA sequence. The method further comprises writing a fourth polynucleotide comprising a fourth DNA sequence onto the flow cell at a third predetermined position, wherein the fourth polynucleotide comprises a third linker sequence of the fourth DNA sequence, wherein the third linker sequence is the reverse complement of at least a portion of the third polynucleotide comprising the third DNA sequence, and a second connecting bridge is formed between the third polynucleotide and the fourth polynucleotide. The method further includes extending at least one of a third polynucleotide and a fourth polynucleotide based on the ligated third polynucleotide and fourth polynucleotide to produce a fifth polynucleotide comprising a fifth DNA sequence that is a combination of the first DNA sequence, the second DNA sequence, and the third DNA sequence, and wherein the fifth polynucleotide has at least 2000 base pairs (bp).

There are variations of any one or more of the above embodiments, wherein the first and second joining sequences are complementary components of a gene of interest being prepared using the method.

There are variations of any one or more of the above embodiments, wherein the distance between the predetermined locations is at least 100 nm.

There are variations of any one or more of the above embodiments, wherein the first and second joining sequences are the reverse complement components of a gene.

In yet another embodiment, another method of producing a polynucleotide is provided. The method comprises writing a first polynucleotide comprising a first DNA sequence onto a flow cell at a first predetermined location, wherein the first polynucleotide comprises a first linker sequence of the first DNA sequence, wherein the flow cell is suitable for sequencing by synthesis, wherein the flow cell comprises a plurality of individual pixels, and wherein the first predetermined location represents a first pixel. The method further comprises writing a second polynucleotide comprising a second DNA sequence onto the flow cell at a second predetermined location, wherein the second polynucleotide comprises a second linker sequence of the second DNA sequence, wherein the second linker sequence is the inverse complement of the first linker sequence, wherein the first linker sequence and the second linker sequence form a first linker bridge between the first polynucleotide and the second polynucleotide, wherein the flow cell is suitable for sequencing by synthesis, wherein the flow cell comprises a plurality of individual pixels, and wherein the second predetermined location represents a second pixel. The method further includes extending at least one of the first polynucleotide and the second polynucleotide based on the ligated first polynucleotide and the second polynucleotide to produce a third polynucleotide comprising a third DNA sequence that is a combination of the first DNA sequence and the second DNA sequence. The method further comprises writing a fourth polynucleotide comprising a fourth DNA sequence onto the flow cell at a third predetermined position, wherein the fourth polynucleotide comprises a third linker sequence of the fourth DNA sequence, wherein the third linker sequence is the reverse complement of at least a portion of the third polynucleotide comprising the third DNA sequence, and a second connecting bridge is formed between the third polynucleotide and the fourth polynucleotide. The method further includes extending at least one of a third polynucleotide and a fourth polynucleotide based on the ligated third polynucleotide and fourth polynucleotide to produce a fifth polynucleotide comprising a fifth DNA sequence that is a combination of the first DNA sequence, the second DNA sequence, and the third DNA sequence, and wherein the fifth polynucleotide has at least 2000 base pairs (bp).

There are variations of any one or more of the above embodiments, wherein the first and second joining sequences are complementary components of a gene of interest being prepared using the method, and wherein the distance between the pixels is at least 100 nm.

It is to be understood that all combinations of the foregoing concepts and other concepts discussed in greater detail below (provided that such concepts do not contradict each other) are to be considered a part of the inventive subject matter disclosed herein, and that the benefits/advantages as described herein are achieved. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are considered part of the inventive subject matter disclosed herein.

Drawings

The details of one or more implementations are set forth in the accompanying drawings and the description below. Other features, aspects, and advantages will become apparent from the description, the drawings, and the claims, wherein:

FIG. 1 depicts a schematic block diagram of an example of a system that can be used to perform biochemical processes;

FIG. 2 depicts a schematic cross-sectional block diagram of an example of a consumable cartridge that may be used with the system of FIG. 1;

FIG. 3 depicts a perspective view of an example of a flow cell that may be used with the system of FIG. 1;

FIG. 4 depicts an enlarged perspective view of a channel of the flow cell of FIG. 3;

FIG. 5 depicts a schematic cross-sectional block diagram of an example of a hole that may be incorporated into the channel of FIG. 4;

FIG. 6 depicts a flow diagram of an example of a method for reading a polynucleotide;

FIG. 7 depicts a schematic cross-sectional block diagram of another example of a hole that may be incorporated into the channel of FIG. 4;

FIG. 8 depicts a flow diagram of an example of a method for writing a polynucleotide;

FIG. 9 depicts a top view of an example of an electrode assembly;

FIG. 10 depicts a schematic cross-sectional block diagram of another example of a hole that may be incorporated into the channel of FIG. 4;

FIG. 11 depicts capture probes generated by writing sequences of interest on a flow cell;

FIG. 12 depicts another method for storing biological information on a flow cell, wherein unique or different indices or barcodes are arranged and written on the flow cell in a predetermined spatial pattern, and wherein the indices or barcodes are used to capture DNA molecules from different portions of a tissue sample;

FIG. 13 depicts the use of certain molecular safety measures to protect data or information stored on a flow cell;

FIG. 14 depicts another method of sample indexing on a flow cell using a variable nucleotide sequence as an identifier;

FIG. 15 depicts a method of using both the P5/P7 primer and the P6/P8 primer on a single flow cell;

FIG. 16 depicts a method of linking two adjacently seeded DNA libraries on a flow cell to provide compound information; and

FIG. 17 depicts a schematic of a synthesized DNA molecule according to one embodiment, in which homopolymer A and complementary homopolymer T are used to stitch two adjacent DNA fragments together.

It will be appreciated that some or all of the figures are schematic representations for purposes of illustration. The drawings are provided for the purpose of illustrating one or more embodiments and it is to be expressly understood that they are not intended to limit the scope or meaning of the claims.

Detailed Description

In some aspects, disclosed herein are methods and systems for DNA storage devices that may be removable and portable and may be used as DNA hard drive modules for archival purposes on a large and small scale. Machine-written DNA may replace conventional forms of data storage (e.g., magnetic, optical, and solid-state storage). In other aspects, disclosed herein are methods for synthesizing polynucleotides (e.g., DNA (or other biological material)) for storing data or other information; and/or reading machine-written polynucleotides such as DNA (or other biological material as defined herein) to retrieve machine-written data or other information. Machine writing of DNA can provide faster read and write speeds, longer data retention times, lower power consumption, and higher data densities. An example of how to store digital information in DNA is disclosed in us publication No. 2015/0261664 entitled "high capacity storage of digital information in DNA" published on 9/17 2015, which is incorporated herein by reference in its entirety. For example, methods from code theory to enhance the recoverability of encoded messages in DNA fragments can be used, including disabling homopolymers of DNA (i.e., runs of multiple identical bases) known to be associated with higher error rates in existing high-throughput techniques. In addition, error detection means similar to parity bits may be integrated into the index information in the code. More sophisticated schemes may be implemented in future developments of DNA storage schemes, including but not limited to error correction codes, and virtually any form of digital data security (e.g., RAID-based schemes) employed in informatics. The DNA encoding of the information can be calculated using software. The bytes comprising each computer file may be represented by a DNA sequence without homopolymers by a coding scheme to generate a coded file that replaces each byte with five or six bases forming the DNA sequence.

Although other encoding schemes may be used, the codes used in the encoding scheme may be constructed to allow direct encoding that approaches the optimal information capacity of a run-length limited channel (e.g., no repeated nucleotides). The resulting computer silicon DNA sequences may be too long to be readily produced by standard oligonucleotide synthesis and may be divided into overlapping segments of 100 bases in length with an overlap of 75 bases. To reduce the risk of systematic synthesis errors that introduce any particular round of bases, the replacement segments of these segments can be converted to their reverse complements, meaning that each base can be "written" four times, twice in each direction. Each section may then be extended with index information and simple error detection information that allows the determination of the computer file from which the section originated and its location in the computer file. The index information may also be encoded as non-repetitive DNA nucleotides and appended to the information storage bases of the DNA segment. The overlap of the length of the 100 bases into the DNA segment with 75 bases is purely arbitrary and illustrative, and it will be appreciated that other lengths and overlaps may be used, and are not limiting.

Other coding schemes for the DNA fragments may be used, for example to provide enhanced error correction properties. The amount of index information may be increased to allow more or larger files to be encoded. An extension to the coding scheme to avoid systematic patterns in DNA segments may be the addition of change information. One way may be to use "shuffling" of information in DNA segments, where the information can be retrieved if the pattern of shuffling is known. Different shuffling patterns can be used for different DNA segments. A further approach is to add a degree of randomness to the information of each DNA segment. For this purpose a series of random numbers can be used, which are modulo-added to the number containing the information encoded in the DNA segment. If the series of random numbers used is known, the information can be retrieved by modulo reduction in the decoding process. Different series of random numbers can be used for different DNA segments. The data-encoded portion of each string may contain Shannon information, 5.07 bits per DNA base, which is close to the theoretical optimum of 5.05 bits per DNA base (for base-4 channels with run length limited to one). Implementation of the index may allow for 314 ═ 4782969 unique data locations. Adding only 2 to 16 index ternary digits (and thus bases) to specify a file and a location within a file can result in a unique location of 316 ═ 43046721, exceeding the actual maximum of 16.8M for the Nested Primer Molecular Memory (NPMM) approach.

The DNA segment design can be synthesized in three different runs (DNA segments randomly assigned to a run) to produce about 1.2X 10 of each DNA segment design⁷And (6) copying. Phosphoramidite chemistry can be used, and inkjet printing and flow cell reactor technology in an in situ microarray synthesis platform can be used. Inkjet printing in a dry room can allow very small amounts of phosphoramidite to be delivered to confined coupling regions on a 2D planar surface, resulting in the parallel addition of hundreds of thousands of bases. Subsequent oxidation and detritylation can be carried out in a flow cell reactor. After completion of DNA synthesis, the oligonucleotide may be cleaved from the surface and deprotected.

Adapters may then be added to the DNA segments to enable the preparation of multiple copies of the DNA fragments. DNA segments without adaptors may require other chemical methods to "prime" chemical synthesis of multiple copies by adding other groups at the end of the DNA segment. Oligonucleotides can be amplified using Polymerase Chain Reaction (PCR) methods and double-ended PCR primers, followed by magnetic bead purification and quantitation. The oligonucleotides can then be sequenced to generate a read of 104 bases. Decoding of the digital information can then be performed by sequencing the central base of each oligonucleotide from both ends, rapid calculation of the full-length oligonucleotide, and removal of sequence reads that are inconsistent with the design. The sequence reads can be decoded using computer software that reverses the encoding method completely. The parity ternary bits indicate an error or sequence reads that may be explicitly decoded or assigned to the reconstructed computer file may be discarded. The position in each decoded file can be detected in a plurality of different sequenced DNA oligonucleotides and any differences caused by DNA synthesis or sequencing errors can be accounted for using simple majority voting.

Although several examples herein are provided in the context of machine-written DNA, it is contemplated that the principles described herein may be applied to other kinds of machine-written biological materials.

As used herein, the term "machine-written DNA" should be understood to encompass one or more strands of a polynucleotide produced by, or modified by, a machine for the storage of data or other information. One example of a polynucleotide herein is DNA. It should be noted that although the term "DNA" is used in the present disclosure in the context of DNA being read or written, this term is used merely as a representative example of a polynucleotide and may encompass the concept of a polynucleotide. As described in more detail herein, a "machine" as used herein with respect to "machine-written" may include an instrument or system specifically designed for writing DNA. The system may be abiotic or biological. In one example, the biological system can comprise or be a polymerase. For example, the polymerase may be terminal deoxynucleotidyl transferase (TdT). In biological systems, the method may additionally be controlled by machine hardware (e.g., a processor) or an algorithm. "machine-written DNA" may comprise any polynucleotide having one or more base sequences written by a machine. Although machine-written DNA is exemplified herein, other polynucleotide strands may be substituted for the machine-written DNA described herein. "machine-written DNA" may include natural bases and modifications of natural bases, including but not limited to bases modified with methylated or other chemical tags, synthetic polymers similar to DNA (e.g., Peptide Nucleic Acids (PNAs)), or morpholino DNA. "machine-written DNA" may also include DNA strands or other polynucleotides formed from at least one base strand derived from nature (e.g., extracted from a naturally occurring organism) and having machine-written base strands immobilized thereon in a parallel or end-to-end manner. In other embodiments. In other embodiments, the "machine-written DNA" may be written by a biological system (e.g., an enzyme) instead of or in addition to the writing of a non-biological system of DNA (e.g., an electrode machine) as described herein. In other words, "machine-written DNA" may be written directly by a machine, or by an algorithm and/or machine-controlled enzyme (e.g., polymerase).

"machine-written DNA" may include data that is converted from an original form (e.g., a photograph, a text document, etc.) to a binary code sequence using known techniques, then the binary code sequence is converted to a DNA base sequence using known techniques, and then the DNA base sequence is produced by a machine in the form of one or more DNA strands or other polynucleotides. Alternatively, "machine-written DNA" may be generated to index or track pre-existing DNA to store data or information from any other source for any suitable purpose, without the intermediate step of converting the raw data into binary code.

As described in more detail below, machine-written DNA may be written to and/or read from the reaction sites. As used herein, the term "reaction site" is a localized region where at least one specified reaction can occur. The reaction site may comprise a support surface of a reaction structure or substrate, onto which a substance may be immobilized. For example, a reaction site may be a discrete region of space in which a discrete set of DNA strands or other polynucleotides are written. The reaction sites may allow for chemical reactions separate from reactions in adjacent reaction sites. An apparatus that provides machine writing of DNA may include a flow cell having a well with a writing feature (e.g., an electrode) and/or a reading feature. In some cases, the reaction site may comprise a surface of the reaction structure (which may be located in a channel of a flow cell) that already has a reaction component thereon, e.g. a polynucleotide colony thereon. In some flow cells, the polynucleotides in a colony have the same sequence, e.g., a clonal copy of a single-stranded or double-stranded template. However, in some flow cells, the reaction site may comprise only a single polynucleotide molecule, e.g., in single-stranded or double-stranded form.

The plurality of reaction sites may be randomly distributed along the reaction structure of the flow cell, or may be arranged in a predetermined manner (e.g., side by side in a matrix (e.g., in a microarray)). The reaction site may also include a reaction chamber, recess, or aperture that at least partially defines a spatial region or volume configured to separate designated reactions. As used herein, the term "reaction chamber" or "reaction recess" includes a defined spatial region of a support structure (which is typically fluidly coupled to a flow channel). The reaction notch may be at least partially separated from the ambient environment or other spatial region. For example, a plurality of reaction notches may be separated from each other by a shared wall. As a more specific example, the reaction notch can be a nanopore that includes an indentation, a pit, a well, a groove, a cavity, or a depression defined by an inner surface of the detection surface and having an opening or a pore (i.e., open-sided) such that the nanopore can be fluidically coupled to the flow channel.

For reading machine-written DNA, one or more discrete detectable regions of the reaction site may be defined. Such detectable regions may be imageable regions, electrically detectable regions, or other types of regions that may have a measurable change in a property (or the absence of a change in a property) based on the type of nucleotide present during reading.

As used herein, the term "pixel" refers to a discrete imageable region. Each imageable region can include spaced apart or discrete regions in which the polynucleotide is present. In some cases, a pixel can include two or more reaction sites (e.g., two or more reaction chambers, two or more reaction recesses, two or more pores, etc.). In other cases, a pixel may include only one reaction site. Each pixel is detected using a corresponding detection device (e.g., an image sensor or other light detection device). The light detecting arrangement may be manufactured using an integrated circuit manufacturing process, such as a process for manufacturing a charge coupled device circuit (CCD) or a Complementary Metal Oxide Semiconductor (CMOS) device or circuit. Thus, the light detecting means may comprise, for example, one or more semiconductor materials, and may take the form of, for example, a CMOS light detecting means (e.g. a CMOS image sensor) or a CCD image sensor (another image sensor). A CMOS image sensor may include an array of light sensors (e.g., photodiodes). In one embodiment, a single image sensor may be used with the objective lens to capture multiple "pixels" during an imaging event. In some other embodiments, each discrete photodiode or photosensor may capture a corresponding pixel. In some embodiments, one or more detection device light sensors (e.g., photodiodes) can be associated with corresponding reaction sites. A light sensor associated with a reaction site can detect light emissions from the associated reaction site. In some embodiments, detection of light emission may be performed via at least one light guide when a specified reaction occurs at the associated reaction site. In some embodiments, multiple light sensors (e.g., several pixels of a light detection or camera device) may be associated with a single reaction site. In some embodiments, a single light sensor (e.g., a single pixel) may be associated with a single reaction site or a group of reaction sites.

As used herein, the term "synthetic" should be understood to include methods in which DNA is produced by a machine to store data or other information. Thus, machine-written DNA may constitute synthetic DNA. As used herein, the terms "consumable cartridge," "kit," "removable cartridge," and/or "cartridge" refer to the same cartridge and/or a combination of components that make up a component for a cartridge or cartridge system. The cartridges described herein may be independent of elements having reaction sites, such as flow cells having a plurality of wells. In some cases, the flow cell may be removably inserted into the cartridge and then inserted into the instrument. In some other embodiments, the flow cell can be removably inserted into the instrument without a cartridge. As used herein, the term "biochemical analysis" may include at least one of biological analysis or chemical analysis.

The term "based on" should be understood to mean that something is determined, at least in part, by what is indicated as "based on". To indicate that something must be completely determined by others, it is described as being based entirely on its completely determined content.

The term "non-nucleotide memory" should be understood to refer to an object, device, or combination of devices capable of storing data or instructions in a form other than nucleotides that can be retrieved and/or processed by the device. Examples of "non-nucleotide memory" include solid-state memory, magnetic memory, hard disk drives, optical drives, and combinations of the foregoing (e.g., magneto-optical storage elements).

The term "DNA storage device" should be understood to refer to an object, device, or combination of devices, such as machine-written DNA, that is configured to store data or instructions in the form of a polynucleotide sequence. Examples of "DNA storage devices" include flow cells having addressable wells as described herein, systems comprising a plurality of such flow cells, and tubes or other containers that store nucleotide sequences that have been cut from their synthetic surfaces. As used herein, the term "nucleotide sequence" or "polynucleotide sequence" is to be understood as encompassing a polynucleotide molecule as well as the underlying sequence of the molecule, depending on the context. The sequence of the polynucleotide may comprise (or encode) information indicative of certain physical characteristics.

The embodiments described herein can be used to perform a specified reaction for the preparation of consumable cartridges and/or biochemical analysis and/or machine-written DNA synthesis.

I. Overview of the System

Fig. 1 is a schematic diagram of a system 100 configured to perform biochemical analysis and/or synthesis. The system 100 can include a base instrument 102 configured to receive and respectively engage a removable cartridge 200 and/or a component (component) having one or more reaction sites. The base instrument 102 and the removable cartridge 200 can be configured to interact with each other to transport the biological material to different locations within the system 100 and/or to perform specified reactions containing the biological material to prepare the biological material for subsequent analysis (e.g., by synthesizing the biological material), and optionally, to detect one or more events of the biological material. In some embodiments, the base instrument 102 can be configured to detect one or more events of biological material directly on the removable cartridge 200. These events may be indicative of a specified reaction containing biological material. The removable cartridge 200 may be configured according to any of the cartridges described herein.

Although reference is made below to base instrument 102 and removable cartridge 200 shown in fig. 1, it should be understood that base instrument 102 and removable cartridge 200 illustrate only one embodiment of system 100 and that other embodiments exist. For example, the base instrument 102 and the removable cartridge 200 include various components and features that collectively perform several operations for preparing and/or analyzing biological material. Further, although the removable cartridge 200 described herein includes an element with a reaction site (e.g., a flow cell with a plurality of wells), other cartridges may be independent of the element with a reaction site, and the element with a reaction site may be inserted into the base instrument 102 separately. That is, in some cases, the flow cell may be removably inserted into the removable cartridge 200, and then the removable cartridge 200 is inserted into the base instrument 102. In some other embodiments, the flow cell may be directly removably inserted into the base instrument 102 without the removable cartridge 200. In further embodiments, the flow cell may be inserted directly into a removable cartridge 200, which removable cartridge 200 is inserted into the base instrument 102.

In the illustrated embodiment, each of the base instrument 102 and the removable cartridge 200 is capable of performing certain functions. However, it should be understood that the base instrument 102 and the removable cartridge 200 may perform different functions and/or may share such functions. For example, the base instrument 102 is shown to include a detection component (assembly)110 (e.g., an imaging device), the detection component 110 configured to detect a specified reaction at the removable cartridge 200. In alternative embodiments, removable cartridge 200 may include a detection assembly and be communicatively coupled to one or more components of base instrument 102. As another example, the base instrument 102 is a "dry" instrument that does not provide liquid to, receive liquid from, and exchange liquid with the removable cartridge 200. That is, as shown, the removable cartridge 200 includes a consumable reagent portion 210 and a flow cell receiving portion 220. The consumable reagent portion 210 can contain reagents used during biochemical analysis and/or synthesis. The flow cell receiving portion 220 can include an optically transparent area or other detectable area for the detection assembly 110 to detect one or more events occurring within the flow cell receiving portion 220. In alternative embodiments, the base instrument 102 can provide, for example, reagents or other liquids to the removable cartridge 200 that are subsequently consumed by the removable cartridge 200 (e.g., for a specified reaction or synthesis procedure).

As used herein, a biological material can include one or more biological or chemical substances, such as nucleosides, nucleotides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, peptides, oligopeptides, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphates, nanopores, organelles, lipid layers, cells, tissues, biologically and/or biologically active compounds (e.g., analogs or mimetics of the foregoing). In some cases, the biological material may include whole blood, lymph, serum, plasma, sweat, tears, saliva, sputum, cerebrospinal fluid, amniotic fluid, semen, vaginal discharge, serous fluid, synovial fluid, pericardial fluid, peritoneal fluid, pleural fluid, transudates, exudates, cystic fluid, bile, urine, gastric fluid, intestinal fluid, stool, single or multi-cell containing fluids, organelle containing fluids, liquefied tissue, liquefied organisms, viruses including viral pathogens, multi-cell organism containing fluids, biological swabs, and biological washes. In some cases, the biological material may include a set of synthetic sequences, including but not limited to machine-written DNA, which may be fixed (e.g., attached in a specific well in a cassette) or unfixed (e.g., stored in a tube).

In some embodiments, the biological material may comprise added materials, such as water, deionized water, saline solutions, acidic solutions, alkaline solutions, detergent solutions, and/or pH buffers. The added material may also contain reagents that will be used to perform biochemical reactions in a given assay protocol. For example, the added liquid may comprise material that is subjected to multiple Polymerase Chain Reaction (PCR) cycles on the biological material. In other aspects, the added material may be a carrier for the biological material (e.g., cell culture media) or other buffering and/or pH adjusting and/or isotonic carriers that may allow or retain the biological function of the biological material.

However, it should be understood that the biological material being analyzed may have a different form or state than the biological material loaded into the system 100 or created by the system 100. For example, the biological material loaded into the system 100 may include whole blood or saliva or a population of cells that are subsequently processed (e.g., by a separation or amplification procedure) to provide prepared nucleic acids. The prepared nucleic acids can then be analyzed (e.g., quantified by PCR or sequenced by SBS) by the system 100. Thus, when the term "biological material" is used in describing a first operation, such as PCR, and the term is used again in describing a subsequent second operation (e.g., sequencing), it should be understood that the biological material in the second operation may be modified relative to the biological material before or during the first operation. For example, amplicon nucleic acids generated from a template nucleic acid amplified in a previous amplification (e.g., PCR) can be sequenced (e.g., SBS). In this case, the amplicon is a copy of the template and the amplicon is present in a higher amount compared to the amount of the template.

In some embodiments, the system 100 may automatically prepare a sample for biochemical analysis based on a substance (e.g., whole blood or saliva or a population of cells) provided by a user. However, in other embodiments, the system 100 may analyze biological material that the user partially or preliminarily prepares for analysis. For example, a user may provide a solution that includes nucleic acids that have been isolated and/or amplified from whole blood. Or a viral sample may be provided in which the RNA or DNA sequences are partially or fully exposed for processing.

As used herein, a "specified reaction" includes a change in at least one of a chemical, electrical, physical, or optical property (or mass) of an analyte of interest. In particular embodiments, the specified reaction is an associated binding event (e.g., incorporation of a fluorescently labeled biomolecule with an analyte of interest). The specified reaction may be a dissociative binding event (e.g., the release of a fluorescently labeled biomolecule from the analyte of interest). The specified reaction may be a chemical transformation, a chemical change, or a chemical interaction. The specified reaction may also be a change in electrical properties. For example, the specified reaction may be a change in ion concentration within the solution. Some reactions include, but are not limited to, chemical reactions such as reduction, oxidation, addition, elimination, rearrangement, esterification, amidation, etherification, cyclization, or substitution; a binding interaction of the first chemical with the second chemical; dissociation reactions in which two or more chemical substances are separated from each other; fluorescence; emitting light; bioluminescence; chemiluminescence; and biological reactions (e.g., nucleic acid replication, nucleic acid amplification, nucleic acid hybridization, nucleic acid ligation, phosphorylation, enzymatic catalysis, receptor binding, or ligand binding). The reaction specified may also be the addition or removal of protons, for example a reaction that can be detected as a change in the pH of the surrounding solution or environment. An additional specified reaction may be the detection of ion flux across a membrane (e.g., a natural or synthetic bilayer membrane). For example, when ions flow through the membrane, the current is broken and the break can be detected. In-situ sensing of charged tags may also be used; thermal sensing and other suitable analytical sensing techniques may also be used.

In particular embodiments, the specified reaction comprises incorporating a fluorescently labeled molecule into the analyte. The analyte may be an oligonucleotide and the fluorescently labeled molecule may be a nucleotide. When excitation light is directed to the oligonucleotide with labeled nucleotides, the designated reaction can be detected and the fluorophore emits a detectable fluorescent signal. In alternative embodiments, the detected fluorescence is the result of chemiluminescence and/or bioluminescence. A given reaction may also increase fluorescence (or) Resonance Energy Transfer (FRET), for example, by bringing a donor fluorophore close to an acceptor fluorophore, by separating the donor and acceptor fluorophores to reduce FRET, by separating a quencher from fluorescein to increase fluorescence, or by co-locating a quencher and fluorophore to reduce fluorescence.

As used herein, "reaction components" include any material that can be used to obtain a specified reaction. For example, reaction components include reagents, catalysts (e.g., enzymes), reactants for the reaction, samples, reaction products, other biomolecules, salts, metal cofactors, chelators, and buffer solutions (e.g., hydrogenation buffers). The reactive components may be delivered to various locations in the fluidic network individually in solution or in one or more mixtures. For example, the reaction components may be delivered to a reaction chamber in which the biological material is immobilized. The reactive component may interact with the biological material directly or indirectly. In some embodiments, removable cartridge 200 is preloaded with one or more reaction components that participate in performing a specified assay protocol. The preloading may be performed at a location (e.g., a manufacturing facility) prior to the user receiving the cartridge 200 (e.g., a customer's facility). For example, one or more reaction components or reagents may be preloaded into the consumable reagent portion 210. In some embodiments, the removable cartridge 200 may also be preloaded with a flow cell in the flow cell receiving portion 220.

In some implementations, the base instrument 102 can be configured to interact with one removable cartridge 200 in each session (session). After the session, the removable cartridge 200 may be replaced with another removable cartridge 200. In other embodiments, the base instrument 102 may be configured to interact with more than one removable cartridge 200 in each session. As used herein, the term "session" includes performing at least one of a sample preparation and/or biochemical analysis protocol. Sample preparation may include synthesizing biological material; and/or separating, isolating, modifying and/or amplifying one or more components of the biological material to render the prepared biological material suitable for analysis. In some embodiments, a session may include a continuous activity in which a plurality of controlled reactions are performed until (a) a specified number of reactions have been performed, (b) a specified number of events have been detected, (c) a specified time period of system time has elapsed, (d) a signal-to-noise ratio has dropped to a specified threshold, (e) a target component has been identified, (f) a system failure or malfunction has been detected; and/or (g) one or more resources used to carry out the reaction have been exhausted. Alternatively, the session may comprise pausing system activity for a period of time (e.g., minutes, hours, days, weeks) and then completing the session until at least one of (a) - (g) occurs.

An assay protocol may include a series of operations for performing, detecting, and/or analyzing a specified reaction. In general, the removable cartridge 200 and the base instrument 102 may include components for performing different operations. The operation of the assay protocol may include fluidic operation, thermal control operation, detection operation, and/or mechanical operation.

Fluidic operations include controlling the flow of fluid (e.g., fluid or gas) through the system 100, which may be actuated by the base instrument 102 and/or the removable cartridge 200. In one example, the fluid is in liquid form. For example, the fluidic operation may include controlling a pump to cause the biological material or reaction components to flow into the reaction chamber.

The thermal control operation may include controlling the temperature of a designated portion of the system 100 (e.g., one or more portions of the removable cartridge 200). For example, the thermal control operation may include increasing or decreasing a temperature of a Polymerase Chain Reaction (PCR) region storing a liquid containing the biological material.

The detecting operation may include controlling activation of the detector or monitoring activity of the detector to detect a predetermined characteristic, quality, or characteristic of the biological material. As one example, the detecting operation may include capturing an image of a designated area including biological material to detect fluorescent emissions from the designated area. The detecting operation may include controlling a light source to illuminate the biological material or controlling a detector to observe the biological material.

The mechanical operation may include controlling a movement or position of a designated member. For example, the mechanical operation may include controlling a motor to move a valve control member in the base instrument 102 that operably engages a movable valve in the removable cartridge 200. In some cases, a combination of different operations may occur simultaneously. For example, the detector may capture an image of the reaction chamber when the pump controls the flow of fluid through the reaction chamber. In some cases, different operations for different biological materials may occur simultaneously. For example, the first biological material may be amplified while the second biological material is being detected (e.g., PCR).

Similar or identical fluidic elements (e.g., channels, ports, reservoirs, etc.) may be labeled differently to more easily distinguish the fluidic elements. For example, a port may be referred to as a reservoir port, a supply port, a network port, a feed port, and the like. It should be understood that two or more fluidic elements (e.g., reservoir channels, sample channels, flow channels, bridge channels) that are labeled differently need not differ in structure. Furthermore, the claims may be modified to add such indicia to more easily distinguish such fluidic elements in the claims.

As used herein, a "liquid" is a relatively incompressible substance and has the ability to flow and conform to the shape of the container or channel in which it is contained. The liquid may be water-based and may include polar molecules that exhibit a surface tension that holds the liquid together. The liquid may also include non-polar molecules, for example in an oil-based or non-aqueous substance. It should be understood that reference to a liquid in this application may include a liquid containing a combination of two or more liquids. For example, separate reagent solutions may be subsequently combined to carry out a given reaction.

One or more embodiments can include retaining the biological material (e.g., template nucleic acid) at a designated location where the biological material is analyzed. As used herein, the term "retained," when used with respect to a biomaterial, includes attaching the biomaterial to a surface or confining the biomaterial within a specified space. As used herein, the term "immobilized," when used with respect to a biological material, includes attaching the biological material to a surface in or on a solid support. Immobilization may include attaching the biological material to the surface at a molecular level. For example, biological materials can be immobilized to the surface of a substrate using techniques that include non-covalent interactions (e.g., electrostatic forces, van der waals forces, and dehydration of hydrophobic interfaces) and covalent bonding, where functional groups or linkers facilitate attachment of the biological materials to the surface. The biological material may be immobilized to the substrate surface based on the characteristics of the substrate surface, the liquid medium carrying the biological material, and the characteristics of the biological material itself. In some cases, the substrate surface may be functionalized (e.g., chemically or physically modified) to facilitate immobilization of the biological material to the substrate surface. The substrate surface may first be modified to have functional groups bound to the surface. The functional group can then bind the biomaterial to immobilize the biomaterial thereon. In some cases, the biomaterial may be immobilized to a surface by a gel.

In some embodiments, nucleic acids can be immobilized to a surface and amplified using bridge amplification. Another useful method for amplifying nucleic acids on a surface is Rolling Circle Amplification (RCA), e.g., using the methods described in further detail below. In some embodiments, nucleic acids can be attached to a surface and amplified using one or more primer pairs. For example, one primer may be in solution while the other primer may be immobilized on a surface (e.g., 5' -linked). For example, a nucleic acid molecule can hybridize to one primer on a surface and then extend the immobilized primer to produce a first copy of the nucleic acid. The primer in solution is then hybridized to a first copy of the nucleic acid, which can be extended using the first copy of the nucleic acid as a template. Optionally, after generating the first copy of the nucleic acid, the original nucleic acid molecule may be hybridized to a second immobilized primer on the surface, and may be extended simultaneously or after primer extension in solution. In any embodiment, an extension repeat run (e.g., amplification) using immobilized primers and primers in solution can be used to provide multiple copies of a nucleic acid. In some embodiments, the biological material can be confined within a predetermined space containing reaction components configured for use during amplification (e.g., PCR) of the biological material.

One or more embodiments described herein may be configured to perform an assay protocol that is or includes an amplification (e.g., PCR) protocol. During an amplification protocol, the temperature of the biological material within the reservoir or channel can be changed to amplify the target sequence or biological material (e.g., DNA of the biological material). For example, the biological material may be subjected to (1) a pre-heating period of about 95 ℃ for about 75 seconds; (2) a denaturation phase at about 95 ℃ for about 15 seconds; (3) an anneal-extension phase of about 59 ℃ for about 45 seconds; (4) the incubation period at about 72 ℃ is about 60 seconds. Embodiments may perform multiple amplification cycles. Note that the above cycle describes only one particular embodiment, and that alternative embodiments may include modifications to the amplification scheme.

The methods and systems described herein may use arrays of features having various densities, including, for example, at least about 10 features/cm²About 100 features/cm²About 500 features/cm²About 1,000 features/cm²About 5,000 features/cm²About 10,000 features/cm²About 50,000 features/cm²About 100,000 features/cm²About 1,000,000 features/cm²About 5,000,000 features/cm²Or higher. The methods and apparatus described herein may include a detection assembly or apparatus having a resolution at least sufficient to resolve individual features at one or more of these densities.

The base instrument 102 can include a user interface 130, the user interface 130 configured to receive user input for performing a specified assay protocol and/or configured to convey information about the assay to a user. The user interface 130 may be integrated with the base instrument 102. For example, the user interface 130 can include a touch screen attached to the housing of the base instrument 102 and configured to recognize a touch from a user and a location of the touch relative to information displayed on the touch screen. Alternatively, the user interface 130 may be remotely located relative to the base instrument 102.

II. box

The removable cartridge 200 is configured to detachably engage or removably couple to the base instrument 102 at the cartridge chamber 140. As used herein, when the terms "detachably engaged" or "removably coupled" (or similar terms) are used to describe the relationship between the removable cartridge 200 and the base instrument 102, the terms are intended to mean that the connection between the removable cartridge 200 and the base instrument 102 is detachable without breaking the base instrument 102. Correspondingly, the removable cartridge 200 may be detachably coupled to the base instrument 102 electrically so that the electrical contacts of the base instrument 102 are not broken. The removable cartridge 200 may be detachably engaged to the base instrument 102 in a mechanical manner such that features of the base instrument 102 that hold the removable cartridge 200 (e.g., the cartridge chamber 140) are not disrupted. The removable cartridge 200 may be detachably coupled to the base instrument 102 in a fluid manner such that the ports of the base instrument 102 are not broken. For example, if only a simple adjustment of a component (e.g., realignment) or a simple replacement (e.g., replacement of a nozzle) is required, the base instrument 102 is deemed not to be "broken". The components (e.g., the removable cartridge 200 and the base instrument 102) can be easily separated when the components can be separated from each other without undue effort or taking a significant amount of time to separate the components. In some embodiments, the removable cartridge 200 and the base instrument 102 can be easily separated without damaging the removable cartridge 200 or the base instrument 102.

In some implementations, the removable cartridge 200 may be permanently modified or partially damaged during a session with the base instrument 102. For example, a container containing a liquid may include a foil lid that is pierced to allow the liquid to flow through the system 100. In such embodiments, the foil lid may be damaged such that the damaged container will be replaced by another container. In certain embodiments, the removable cartridge 200 is a disposable cartridge such that the removable cartridge 200 can be replaced and optionally disposed of after a single use. Similarly, the flow cells of removable cartridge 200 may be individually disposable such that the flow cells may be replaced and optionally disposed of after a single use.

In other embodiments, the removable cartridge 200 can be used more than once while engaged with the base instrument 102, and/or can be removed from the base instrument 102, reloaded with reagents, and re-engaged to the base instrument 102 for other specified reactions. Thus, in some cases, the removable cartridge 200 may be retrofitted such that the same removable cartridge 200 may be used with different consumables (e.g., reactive components and biological materials). After the cartridge 200 has been removed from the base instrument 102 at the customer facility, it may be refurbished at the manufacturing facility.

The cartridge compartment 140 may include slots, seats, connector interfaces, and/or any other features to receive the removable cartridge 200 or a portion thereof to interact with the base instrument 102.

The removable cartridge 200 may include a fluidic network that may hold and direct a fluid (e.g., a liquid or a gas) therethrough. The fluid network may include a plurality of interconnected fluid elements capable of storing fluid and/or allowing fluid to flow therethrough. Non-limiting examples of fluidic elements include channels, ports of channels, cavities, storage devices, reservoirs of storage devices, reaction chambers, waste reservoirs, detection chambers, multi-purpose chambers for reactions and detections, and the like. For example, the consumable reagent portion 210 can include one or more reagent wells or chambers that store reagents, and can be part of or coupled to a fluidic network. The fluidic elements can be fluidically coupled to one another in a prescribed manner such that the system 100 is capable of sample preparation and/or analysis.

As used herein, the term "fluidly coupled" (or similar terms) means that two spatial regions are connected together such that a liquid or gas can be directed between the two spatial regions. In some cases, the fluid coupling allows fluid to be directed back and forth between two spatial regions. In other cases, the fluid coupling is unidirectional such that there is only one direction of flow between the two spatial regions. For example, the assay reservoir can be fluidly coupled to the channel such that a liquid can be transported from the assay reservoir into the channel. However, in some embodiments, fluid in the channel may not be directed back to the assay reservoir. In particular embodiments, the fluidic network may be configured to receive biological material and direct the biological material through sample preparation and/or sample analysis. The fluidic network can direct the biological material and other reactive components to the waste reservoir.

Fig. 2 depicts an embodiment of a consumable cartridge 300. The consumable cartridge may be part of a combined removable cartridge (e.g., consumable reagent portion 210 of removable cartridge 200 of fig. 1) or may be a separate kit. The consumable cartridge 300 may include a housing 302 and a top 304. The housing 302 may comprise a non-conductive polymer or other material and be formed to construct one or more reagent chambers 310, 320, 330. The size of the reagent chambers 310, 320, 330 may be varied to accommodate different volumes of reagent to be stored therein. For example, the first chamber 310 may be larger than the second chamber 320, and the second chamber 320 may be larger than the third chamber 330. The first chamber 310 is sized to accommodate a larger volume of a particular reagent, such as a buffer reagent. The second chamber 320 may be sized to contain a smaller reagent volume than the first chamber 310, e.g., a reagent chamber containing a lysis reagent. The third chamber 330 may be sized to hold an even smaller volume of reagent than the first and second chambers 310, 320, such as a reagent chamber holding a reagent containing fully functional nucleotides.

In the illustrated embodiment, the housing 302 has a plurality of housing walls or sides 350 that form the chambers 310, 320, 330 therein. In the illustrated embodiment, the housing 302 forms an at least substantially unitary or monolithic structure. In alternative embodiments, housing 302 may be constructed from one or more subcomponents that are combined to form housing 302, such as independently formed compartments of chambers 310, 320, and 330.

Once reagents are provided into the respective chambers 310, 320, 330, the housing 302 may be sealed by the top 304. The top 304 may comprise a conductive or non-conductive material. For example, the top 304 may be an aluminum foil seal that is adhered to the top surface of the housing 302 to seal the reagents within their respective chambers 310, 320, 330. In other embodiments, the top 304 may be a plastic seal that is adhered to the top surface of the housing 302 to seal the reagents within their respective chambers 310, 320, 330.

In some embodiments, the housing 302 can also contain an identifier 390. The identifier 390 may be a Radio Frequency Identification (RFID) transponder, a bar code, an identification chip, and/or other identifier. In some embodiments, the identifier 390 may be embedded in the housing 302 or attached to an exterior surface. The identifier 390 may contain data for a unique identifier of the consumable cartridge 300 and/or data for the type of consumable cartridge 300. The data of the identifier 390 may be read by the base instrument 102 or a separate device configured to heat the consumable cartridge 300 as described herein.

In some embodiments, the consumable cartridge 300 may include other components, such as valves, pumps, fluid lines, ports, and the like. In some embodiments, the consumable cartridge 300 can be housed within an additional outer housing.

System controller

The base instrument 102 can also include a system controller 120, the system controller 120 configured to control operation of at least one of the removable cartridge 200 and/or the detection assembly 110. The system controller 120 may be implemented using any combination of dedicated hardware circuitry, boards, DSPs, processors, etc. Alternatively, the system controller 120 may be implemented using an off-the-shelf PC having a single processor or multiple processors, with functional operations distributed among the processors. As a further alternative, the system controller 120 may be implemented using a hybrid configuration in which some modular functions are performed using dedicated hardware, while the remaining modular functions are performed using an off-the-shelf PC or the like.

The system controller 120 may include a plurality of circuit modules configured to control the operation of certain components of the base instrument 102 and/or the removable cartridge 200. The term "module" herein may refer to a hardware device configured to perform a specific task. For example, the circuit module may include a flow control module configured to control the flow of fluid through the fluid network of the removable cartridge 200. The flow control module may be operably coupled to the valve actuator and/or the system pump. The flow control module may selectively activate the valve actuator and/or the system pump to cause fluid to flow through one or more paths and/or prevent fluid from flowing through one or more paths.

The system controller 120 may also include a thermal control module. The thermal control module may control a thermal cycler or other thermal component to provide and/or remove thermal energy from the sample preparation region of the removable cartridge 200 and/or any other region of the removable cartridge 200. The thermal cycler can increase and/or decrease the temperature experienced by the biological material according to a PCR protocol.

The system controller 120 can also include a detection module configured to control the detection assembly 110 to obtain data about the biological material. If the detection assembly 110 is part of the removable cartridge 200, the detection module may control the operation of the detection assembly 110 through a direct wired connection or through a contact array. The detection module may control the detection component 110 to acquire data at a predetermined time or within a predetermined time period. For example, when the biological material has a fluorophore attached thereto, the detection module can control the detection assembly 110 to capture an image of the reaction chamber of the flow cell receiving portion 220 of the removable cartridge. In some embodiments, multiple images may be obtained.

Optionally, the system controller 120 may include an analysis module configured to analyze the data to provide at least partial results to a user of the system 100. For example, the analysis module can analyze imaging data provided by the detection component 110. The analysis may include identifying a nucleic acid sequence of the biological material.

The system controller 120 and/or circuit modules described above may include one or more logic-based devices including one or more microcontrollers, processors, Reduced Instruction Set Computers (RISC), Application Specific Integrated Circuits (ASICs), Field Programmable Gate Arrays (FPGAs), logic circuits, and any other circuit capable of executing the functions described herein. In one embodiment, the system controller 120 and/or circuit modules execute a set of instructions stored in a computer or machine readable medium to perform one or more assay protocols and/or other operations. The set of instructions may be stored in the form of an information source or physical memory element within the base instrument 102 and/or the removable cartridge 200. The protocols performed by the system 100 may be used to perform, for example, machine-written DNA or synthetic DNA (e.g., converting binary data into a DNA sequence and then synthesizing DNA strands or other polynucleotides representing the binary data), quantitative analysis of DNA or RNA, protein analysis, DNA sequencing (e.g., sequencing-by-synthesis (SBS)), sample preparation, and/or preparation of a library of fragments for sequencing.

The set of instructions may include various commands that instruct the system 100 to perform specific operations, such as the methods and processes of the various embodiments described herein. The set of instructions may be in the form of a software program. As used herein, the terms "software" and "firmware" are interchangeable, and include any computer program stored in memory for execution by a computer, including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory. The above memory types are examples only, and are thus not limiting as to the types of memory usable for storage of a computer program.

The software may be in various forms, such as system software or application software. Further, the software may be in the form of a collection of separate programs, or a program module or portion of a program module within a larger program. The software may also include modular programming in the form of object-oriented programming. After obtaining the detection data, the detection data may be automatically processed by the system 100, processed in response to user input, or processed in response to a request made by another processor (e.g., a remote request over a communication link).

The system controller 120 may be connected to other components or subsystems of the system 100 via a communication link, which may be hardwired or wireless. The system controller 120 may also be communicatively connected to a displaced system or server. The system controller 120 may receive user inputs or commands from the user interface 130. The user interface 130 may include a keyboard, mouse, touch screen panel, and/or voice recognition system, among others.

The system controller 120 may be used to provide processing capabilities, such as storing, understanding, and/or executing software instructions and controlling the overall operation of the system 100. The system controller 120 may be configured and programmed to control data and/or power aspects of the various components. Although the system controller 120 is represented in fig. 1 as a single structure, it should be understood that the system controller 120 may include a plurality of individual components (e.g., processors) that are distributed throughout the system 100 at various locations. In some embodiments, one or more components may be integrated with base instrument 102, and one or more components may be remotely located relative to base instrument 102.

Flow cell

Fig. 3-4 illustrate an example of a flow cell 400 that may be used with the system 100. The flow cell of this example includes a body defining a plurality of elongate flow channels 410 that are recessed below the upper surface 404 of the body 402. The flow channels 410 are generally parallel to each other and extend along substantially the entire length of the body 402. Although five flow channels 410 are shown, the flow cell 400 may include any other suitable number of flow channels 410, including more or less than five flow channels 410. The flow cell 400 of this example also includes a set of inlet ports 420 and a set of outlet ports 422, where each port 420, 422 is associated with a corresponding flow channel 410. Thus, each inlet port 420 may be utilized to communicate fluid (e.g., reagents, etc.) to a corresponding channel 410; and each outlet port 422 may be used to communicate fluid from a corresponding flow channel 410.

In some versions, the flow cell 400 is integrated directly into the flow cell receiving portion 220 of the removable cartridge 200. In some other versions, the flow cell 400 is removably coupled with the flow cell receiving portion 220 of the removable cartridge. In versions where the flow cell 400 is directly integrated into the flow cell receiving portion 220 or removably coupled to the flow cell receiving portion 220, the flow channel 410 of the flow cell 400 may receive fluid from the consumable reagent portion 210 through the inlet port 420, and the inlet port 420 may be fluidly coupled to a reagent stored in the consumable reagent portion 210. Of course, the flow channel 410 may be coupled to various other fluid sources or reservoirs, etc. via the ports 420, 422. As another illustrative variation, some versions of the consumable cartridge 300 may be configured to removably receive or otherwise integrate the flow cell 400. In such a version, the flow channel 410 of the flow cell 400 may receive fluid from the reagent chambers 310, 320, 330 through the inlet port 420. Other suitable ways in which the flow cell 400 may be incorporated into the system 100 will be apparent to those skilled in the art based on the teachings herein.

Fig. 4 shows the flow channel 410 of the flow cell 400 in more detail. As shown, the flow channel 410 includes a plurality of apertures 430 formed in the bottom surface 412 of the flow channel 410. As will be described in more detail below, each well 430 is configured to contain a DNA strand or other polynucleotide, such as a machine-written polynucleotide. In some versions, each bore 430 has a cylindrical configuration with a generally circular cross-sectional profile. In some other versions, each aperture 430 has a polygonal (e.g., hexagonal, octagonal, etc.) cross-sectional profile. Alternatively, the apertures 430 may have any other suitable configuration. It should also be understood that the apertures 430 may be arranged in any suitable pattern, including but not limited to a grid pattern.

Fig. 5 shows a portion of a channel within a flow cell 500, which is an example of a variation of flow cell 400. The channel depicted in fig. 5 is a variation of the flow channel 410 of the flow cell 400. The flow cell 500 may be operated to read the polynucleotide strand 550, the polynucleotide strand 550 being immobilized to the bottom 534 of the well 530 in the flow cell 500. By way of example only, the bottom 534 of the immobilized polynucleotide strand 550 may comprise a co-block polymer that is end-capped with an azide group. As a further example only, such polymers may include a poly (N- (5-azidoacetamidopentyl) acrylamide-co-acrylamide) (PAZAM) coating provided in accordance with at least some of the teachings in U.S. patent No. 9,012,022 entitled "polymer coating" published on 21/4/2015, the entire contents of which are incorporated herein by reference. Such polymers may be incorporated into any of the various flow cells described herein.

In this example, the apertures 530 are separated by interstitial spaces 514 provided by the bottom surface 512 of the flow cell 500. Each cell 530 has a sidewall 532 and a bottom 534. The flow cell 500 in this example can be operated to provide an image sensor 540 under each aperture 530. In some versions, each aperture 530 has at least one corresponding image sensor 540, the image sensors 540 being fixed in position relative to the aperture 530. Each image sensor 540 may comprise a CMOS image sensor, a CCD image sensor, or any other suitable kind of image sensor. By way of example only, each aperture 530 may have one associated image sensor 540 or a plurality of associated image sensors 540. As another variation, a single image sensor 540 may be associated with two or more apertures 530. In some versions, one or more image sensors 540 are moved relative to aperture 530 such that a single image sensor 540 or a single group of image sensors 540 can be moved relative to aperture 530. As yet another variation, flow cell 500 may be movable relative to a single image sensor 540 or a single group of image sensors 540 that may be at least substantially fixed in position.

Each image sensor 540 may be integrated directly into the flow cell 500. Alternatively, each image sensor 540 may be integrated directly into a cartridge, such as the removable cartridge 200, with the flow cell 500 integrated into or coupled to the flow cell. As yet another illustrative variation, each image sensor 540 may be integrated directly into the base instrument 102 (e.g., as part of the detection assembly 110 described above). Wherever the image sensor 540 is located, the image sensor 540 may be integrated into a printed circuit that includes other components (e.g., control circuitry, etc.). In versions where one or more image sensors 540 are not directly integrated into the flow cell 500, the flow cell 500 may include optical transmission features (e.g., windows, etc.) that allow the one or more image sensors 540 to capture fluorescence emitted by the one or more fluorophores. As described in more detail below, the one or more fluorophores are associated with polynucleotide strand 550 and immobilized onto bottom 534 of well 530 in flow cell 500. It should also be understood that various optical elements (e.g., lenses, optical waveguides, etc.) may be positioned between the bottom 534 of aperture 530 and the corresponding image sensor 540.

As also shown in FIG. 5, the light source 560 is operable to project light 562 into the aperture 530. In some versions, each aperture 530 has at least one corresponding light source 560, wherein the light sources 560 are fixed in position relative to the aperture 530. By way of example only, each aperture 530 may have one associated light source 560 or a plurality of associated light sources 560. As another variation, a single light source 560 may be associated with two or more apertures 530. In some other versions, one or more light sources 560 are moved relative to aperture 530 such that a single light source 560 or group of light sources 560 can be moved relative to aperture 530. As yet another variation, the flow cell 500 may be movable relative to a single light source 560 or a single set of light sources 560, which single light source 560 or single set of light sources 560 may be substantially fixed in position. By way of example only, each light source 560 may include one or more lasers. In another example, the light source 560 may include one or more diodes.

Each light source 560 can be integrated directly into the flow cell 500. Alternatively, each light source 560 can be integrated directly into a cartridge (e.g., removable cartridge 200) into which the flow cell 500 is integrated or coupled. As yet another illustrative variation, each light source 560 may be integrated directly into base instrument 102 (e.g., as part of detection assembly 110 described above). In versions where the one or more light sources 560 are not directly integrated into the flow cell 500, the flow cell 500 may include optically transmissive features (e.g., windows, etc.) that allow the well 530 to receive light emitted by the one or more light sources 560, thereby enabling the light to reach the polynucleotide strand 550 immobilized on the bottom 534 of the well 530. It is also understood that various optical elements (e.g., lenses, optical waveguides, etc.) may be interposed between apertures 530 and corresponding light sources 560.

As described elsewhere herein, and as shown in block 590 of fig. 6, the DNA reading method can begin with performing a sequencing reaction in target well 530 (e.g., according to at least some teachings of U.S. patent No. 9,453,258 entitled "methods and compositions for nucleic acid sequencing," published on 9/27 2016 (which is incorporated herein by reference in its entirety)). Next, as shown in block 592 of FIG. 6, a light source 560 is activated on the targeting orifice 530, thereby illuminating the targeting orifice 530. Projected light 562 can cause fluorophores associated with polynucleotide strand 550 to fluoresce. Accordingly, as shown in block 594 of fig. 6, the corresponding image sensor 540 may detect fluorescence emitted from one or more fluorophores associated with the polynucleotide strand 550. The system controller 120 of the base instrument 102 may drive the light source 560 to emit light. The system controller 120 of the base instrument 102 can also process image data obtained from the image sensor 540 representing the fluorescence emission profile of the polynucleotide strands 550 in the wells 530. As shown in block 596 of fig. 6, the system controller 120 can determine the base sequence in each polynucleotide strand 550 by using image data from the image sensor 540. By way of example only, the methods and apparatus may be utilized to map a genome or otherwise determine biological information associated with a naturally occurring organism from which or based on which DNA strands or other polynucleotides were obtained. Alternatively, as will be described in more detail below, the above-described methods and apparatus may be utilized to obtain data stored in machine-written DNA.

By way of further example only, when performing the procedure shown in fig. 6 above, a spatiotemporal sequencing reaction may utilize one or more chemical and imaging events or steps to distinguish between multiple analytes (e.g., four nucleotides) incorporated into a growing nucleic acid strand during a sequencing reaction. Alternatively, less than four different colors may be detected in a mixture with four different nucleotides, while still allowing the determination of four different nucleotides (e.g., in a sequencing reaction). A pair of nucleotide types can be detected at the same wavelength, but can be distinguished based on differences in intensity of one member of the pair relative to the other member, or based on changes in one member of the pair (resulting in the appearance or disappearance of a distinct signal compared to the other member of the pair detected), e.g., by chemical, photochemical, or physical modification.

V. machine-written biomaterial

In some embodiments, a system 100 (e.g., the system 100 shown in fig. 1) can be configured to synthesize biological material (e.g., polynucleotides (e.g., DNA)) to encode data that can be later retrieved by performing the above-described assays. In certain embodiments, such encoding may be performed by assigning values to nucleotide bases (e.g., binary values (e.g., 0 or 1), ternary values (e.g., 0, 1, or 2, etc.)), which converts the data to be encoded into a string of related values (e.g., converting a text message into a binary string using an ASCII encoding scheme), and then creating one or more polynucleotides composed of nucleotides of bases, the sequence corresponding to the string obtained by converting the data.

In some embodiments, the generation of such polynucleotides may be performed using a version of flow cell 400 having an array of wells 630 configured as shown in fig. 7. Fig. 7 shows a portion of a channel within a flow cell 600, which is an example of a variation of the flow cell 400. In other words, the channel depicted in fig. 7 is a variation of the flow channel 410 of the flow cell 400. In this example, each aperture 630 is recessed below the bottom surface 612 of the flow cell 600. Thus, the holes 630 are spaced apart from each other by the interstitial spaces 614. By way of example only, the apertures 630 may be arranged in a grid or any other suitable pattern along the bottom surface 612 of the flow cell 600. Each aperture 630 of this example includes a sidewall 632 and a bottom 634. Each aperture 630 of this example also includes a corresponding electrode assembly 640 located on the bottom 634 of the aperture 630. In some versions, each electrode assembly 640 includes only a single electrode element. In some other versions, each electrode assembly 640 includes a plurality of electrode elements or segments. The terms "electrode" and "electrode assembly" are to be understood herein as being interchangeable.

The base instrument 102 is operable to independently activate the electrode assemblies 640 such that one or more electrode assemblies 640 may be in an activated state while one or more other electrode assemblies 640 are not. In some versions, a CMOS device or other device is used to control the electrode assembly 640. Such CMOS devices may be integrated directly into the flow cell 600, may be integrated into a cartridge (e.g., cartridge 200) that integrates the flow cell 600, or may be integrated directly into the base instrument 102. As shown in fig. 7, each electrode assembly 640 extends along the entire width of the bottom portion 634, terminating at a side wall 632 of the corresponding aperture 630. In other versions, each electrode assembly 640 may extend along only a portion of the base portion 634. For example, some versions of the electrode assembly 640 may terminate internally with respect to the side wall 632. Although the electrode assemblies 540 are schematically depicted in fig. 5 as a single element, it should be understood that each electrode assembly 540 may actually be formed from a plurality of discrete electrodes, rather than being composed of only a single electrode.

As shown in fig. 7, an acid that can deprotect the end groups of polynucleotide strands 650 in wells 630 can be electrochemically generated by activating the electrode assemblies 640 of the associated wells 630 to generate specific polynucleotide strands 650. By way of illustration, the polynucleotide strand 650 can be chemically attached to the surface at the bottom of the well 630 using a linker having chemical properties such as silane chemistry at one end and compatible with DNA synthesis at the other end (e.g., short oligonucleotides for enzyme binding).

To facilitate reagent exchange (e.g., the transfer of a deblocking agent), in this example, each electrode assembly 640 and the bottom 634 of each well 630 can include at least one opening 660. The opening 660 may be fluidly coupled with a flow passage 662 extending below the aperture 630 below the bottom 634. To provide such an opening 660 through the electrode assembly 640, the electrode assembly 640 may be annular, may be placed in quadrants, may be placed on the perimeter or sidewall 632 of the well 630, or may be placed or shaped in other suitable ways to avoid interfering with reagent exchange and/or passage of light (e.g., as may be used in sequencing processes involving detection of fluorescence emissions). In other embodiments, reagents may be provided into the flow channel of the flow cell 600 without the opening 660. It should be understood that the opening 660 may be optional and may be omitted in some versions. Similarly, the flow passage 662 may be optional and may be omitted in some versions.

Fig. 9 shows an example of the form that electrode assembly 640 may take. In this example, the electrode assembly 640 includes four discrete electrode segments 642, 644, 646, 648 that together define an annular shape. The electrode segments 642, 644, 646, 648 are thus configured as discrete but adjacent quadrants of a ring. Each electrode segment 642, 644, 646, 648 may be configured to provide a predetermined charge uniquely associated with a particular nucleotide. For example, electrode segment 642 may be configured to provide a charge uniquely associated with adenine; electrode segment 644 can be configured to provide a charge uniquely associated with cytosine; electrode segment 646 can be configured to provide a charge uniquely associated with guanine; the electrode segments 648 may be configured to provide a charge uniquely associated with thymine. When the mixture of four nucleotides flows through the flow channel above the aperture 630, activation of the electrode segments 642, 644, 646, 648 can cause the corresponding nucleotides from the flow to adhere to the strand 650. Thus, when electrode segment 642 is activated, it can proceed to write adenine to strand 650. When electrode segment 644 is activated, it can proceed to write cytosine to chain 650; when electrode segment 646 is activated, it can proceed to write guanine to strand 650; when the electrode segment 648 is activated, it can proceed to write thymine to the chain 650. This writing may be provided by hybridization of the activated electrode segment 642, 644, 646, 648 to an inhibitor of the enzyme of the pixel with which the activated electrode segment 642, 644, 646, 648 is associated. Although the electrode segments 642, 644, 646, 648 are shown in fig. 9 as forming a ring shape, it should be understood that any other suitable shape may be formed by the electrode segments 642, 644, 646, 648. In other embodiments, a single electrode may be used for the electrode assembly 640, and the charge may be adjusted to incorporate multiple nucleotides to be written to a DNA strand or other polynucleotide.

As another example, the electrode assembly 640 may be activated to provide a localized (e.g., within the aperture 630 in which the electrode assembly 640 is disposed) electrochemically generated pH change; and/or electrochemically generating a localized moiety (e.g., a reducing or oxidizing agent) to remove the blocking agent from the nucleotide. As another variation, different nucleotides may have different blocking agents. These blocking agents may be photo-cleaved based on the wavelength of light delivered to the aperture 630 (e.g., light 562 projected from the light source 560). As another variation, different nucleotides may have different blocking agents. And those blocking agents may be cleaved based on certain other conditions. For example, one of the four blocking agents can be removed based on a combination of reducing conditions plus an upper local pH or a lower local pH. Based on the combination of the oxidation conditions plus the high local pH or the low local pH, the other of the four blocks can be removed; depending on the combination of light and high local pH, another of the four blocks may be removed. The other of the four blocks can be removed based on a combination of light and low local pH. Thus, four nucleotides can be incorporated simultaneously, but selective deblocking, which occurs in response to four different sets of conditions, is used.

The electrode assembly 640 further defines an opening 660 at the center of the arrangement of electrode segments 642, 644, 646, 648. As described above, the opening 660 may provide a path for fluid communication between the flow channel 662 and the bore 630, thereby allowing reagents or the like flowing through the flow channel 662 to reach the bore 630. As noted above, some variations may omit the flow passage 662 and provide communication for reagents or the like to reach the wells 630 in some other manner (e.g., by passive diffusion or the like). As described herein, the opening 660 can provide a path for light transmission through the bottom of the aperture 630 during a read cycle, regardless of whether the fluid is communicated through the opening 660. In some versions, opening 660 may be optional and thus may be omitted. In versions where the opening 660 is omitted, fluid may be delivered to the aperture 630 via one or more flow channels above the aperture 630 or positioned relative to the aperture 630. Furthermore, the opening 660 may not be needed to provide a path for light transmission through the bottom of the aperture 630 during a read cycle. For example, as described below with respect to flow cell 601, electrode assembly 640 can comprise an optically transparent material (e.g., an optically Transparent Conductive Film (TCF), etc.), and flow cell 600 can itself comprise an optically transparent material (e.g., glass), such that electrode assembly 640 and the material forming flow cell 600 can allow fluorescence emitted from one or more fluorophores associated with machine-written polynucleotide strand 650 to reach image sensor 540 located below well 630.

Fig. 8 shows an example of a method that can be used for machine-writing of polynucleotides or other nucleotide sequences in a flow cell 600. At the beginning of the method, nucleotides may flow into the flow cell 600, through the well 630, as shown in the first block 690 of fig. 8. The electrode assembly 640 can then be activated to write the first nucleotide to the primer at the bottom of the target well 630, as shown in the next block 692 of fig. 8. As shown in the next box 694 of FIG. 8, a terminator may then be cleaved off from the first nucleotide that was just written in the target well 630. Various suitable ways in which the terminator may be cleaved from the first nucleotide will be apparent to those skilled in the art based on the teachings herein. Once the terminator is cleaved from the first nucleotide, as shown in the next block 696 of fig. 8, the electrode assembly 640 may be activated to write the second nucleotide to the first nucleotide. Although not shown in FIG. 8, the terminator can be cleaved from the second nucleotide, then the third nucleotide can be written to the second nucleotide, and so on until the desired nucleotide sequence has been written.

In some embodiments, data encoding via synthesis of biological material (e.g., DNA) may be performed in other ways. For example, in some embodiments, the flow cell 600 may lack the electrode assembly 640 entirely. For example, the deblocking agent may be selectively communicated from the flow channel 662 to the aperture 630 through an opening 660. This may eliminate the need for the electrode assembly 640 to selectively activate nucleotides. As another example, an array of wells 630 can be exposed to a solution containing all nucleotide bases that can be used to encode data, and individual nucleotides can then be selectively activated for individual wells 630 by using light from a Spatial Light Modulator (SLM). As another example, in certain embodiments, individual bases may be assigned a combined value (e.g., adenine may be used to encode binary couplet 00, guanine may be used to encode binary couplet 01, cytosine may be used to encode binary couplet 10, and thymine may be used to encode binary couplet 11) to increase the storage density of the resulting polynucleotide. Other examples are possible and will be apparent to those skilled in the art based on this disclosure. Accordingly, the above description of synthesizing biological material (e.g., DNA) to encode data should be understood to be illustrative only and should not be taken as limiting.

Reading machine-written biological materials

After the polynucleotide chain 650 has been machine written in one or more wells 630 of the flow cell 600, the polynucleotide chain 650 can then be read to extract any data or other information stored in the machine-written polynucleotide chain 650. Such a reading method may be performed using an arrangement such as that shown in fig. 5 and described above. In other words, one or more light sources 560 may be used to illuminate one or more fluorophores associated with the machine-written polynucleotide strand 650; and, one or more image sensors 540 may be used to detect fluorescence emitted by the illuminated one or more fluorophores associated with the machine-written polynucleotide strand 650. The fluorescent distribution of light emitted by the illuminated fluorophore or fluorophores associated with polynucleotide strand 650 can be processed to determine the base sequence in machine-written polynucleotide strand 650. The determined base sequence in the machine-written polynucleotide strand 650 can be processed to determine data or other information stored in the machine-written polynucleotide strand 650.

In some versions, the machine-written polynucleotide strands 650 are retained in the flow cell 600 comprising the wells 630 for a storage period. Flow cell 600 can allow machine-written polynucleotide strands 650 to be read directly from the flow cell when it is desired to read machine-written polynucleotide strands 650. By way of example only, a flow cell 600 comprising a well 630 can be received in a cartridge (e.g., cartridge 200) or base instrument 102 comprising a light source 560 and/or an image sensor 540 such that a machine-written polynucleotide strand 650 is read directly from the well 630.

As another illustrative example, a flow cell containing an aperture 630 may incorporate one or both of the light source 560 or the image sensor 540 directly. Fig. 10 shows an example of a flow cell 601, the flow cell 601 comprising an aperture 630 with an electrode assembly 640, one or more image sensors 540 and a control circuit 670. As in flow cell 500 depicted in fig. 5, flow cell 601 of this example is operable to receive light 562 projected from light source 560. The projected light 562 can fluoresce one or more fluorophores associated with the machine-written polynucleotide strand 650; and, the corresponding one or more image sensors 540 can capture fluorescence emitted from one or more fluorophores associated with the machine-written polynucleotide strand 650.

As noted above in the context of flow cell 500, each well 650 of flow cell 601 may include its own image sensor 540 and/or light source 560; or the components may be otherwise configured and arranged as described above. In this example, fluorescence emitted from one or more fluorophores associated with the machine-written polynucleotide strand 650 can reach the image sensor 540 through the opening 660. Additionally or alternatively, electrode assembly 640 can include an optically transparent material (e.g., an optically Transparent Conductive Film (TCF), etc.), and flow cell 601 itself can comprise an optically transparent material (e.g., glass), such that electrode assembly 640 and the material forming flow cell 601 can allow fluorescence emitted from one or more fluorophores associated with machine-written polynucleotide strand 650 to reach image sensor 540. In addition, various optical elements (e.g., lenses, optical waveguides, etc.) may be placed between the wells 650 and the corresponding image sensor(s) to ensure that the image sensor 540 only receives fluorescence emitted from one or more fluorophores associated with the machine-written polynucleotide strands 650.

In this example, control circuitry 670 is integrated directly into flow cell 601. By way of example only, the control circuitry 670 may include a CMOS chip and/or other printed circuit configurations/components. The control circuitry 670 may be in communication with the image sensor 540, the electrode assembly 640, and/or the light source 560. In this case, "communication" means that the control circuitry 670 is in electrical communication with the one or more image sensors 540, the one or more electrode assemblies 640, and/or the light source 560. For example, the control circuitry 670 may be operable to receive and process signals from one or more image sensors 540 that represent images received by the image sensors 540. In this context, "in communication" may also include control circuitry 670 that provides power to the image sensor 540, the electrode assembly 640, and/or the light source 560.

In some versions, each image sensor 540 has a corresponding control circuit 670. In some other versions, control circuitry 670 is coupled to multiple (if not all) image sensors in flow cell 601. Various components and configurations that may be used to implement them will be apparent to those skilled in the art based on the teachings herein. It is also understood that the control circuitry 670 may be fully or partially integrated into the cartridge (e.g., the removable cartridge 200) and/or the base instrument 102 in addition to or instead of being integrated into the flow cell 601.

As yet another illustrative example, machine-written polynucleotide strand 650 can be transferred from well 630 after synthesis, whether using a write-only flow cell, such as flow cell 600 of fig. 7, or a read-write flow cell, such as flow cell 601 of fig. 10. This may occur shortly after synthesis is complete (before reading the machine-written polynucleotide chain 650 or at any other suitable time). In such a version, machine-written polynucleotide strands 650 can be transferred to a read-only flow cell similar to flow cell 500 shown in fig. 5; and then read in the read-only flow cell 500. Alternatively, any other suitable device or method may be used.

In some embodiments, reading data encoded by the synthesis of biological material may be accomplished by determining wells 630 that store synthesized chains of interest 650, and then sequencing those chains 650 using techniques such as those previously described (e.g., sequencing-by-synthesis). In some embodiments, to facilitate reading of data stored in a nucleotide sequence, the index may be updated with information of the display well 630 as the data is stored, wherein the chain 650 encoding the data is synthesized. For example, when storing a 1 megabit (1,048,576 bits) file using an embodiment of the system 100 configured to synthesize a chain 650 capable of storing up to 256 bits of data, the system controller 120 may perform, for example, the following steps: 1) dividing the file into 4,096256 bit segments; 2) identifying a sequence of 4,096 wells 630 in the flow cell 600, 601 that are not currently being used to store data; 3) write 4,096 segments to 4,096 holes 430, 530; 4) the index is updated to indicate that the sequence starting from the first identified hole 630 to the end of the last identified hole 630 is being used to store the file. Subsequently, when a request is made to read a file, the index can be used to identify the wells 630 containing the relevant chains 650, the chains 650 from those wells 630 can be sequenced, and the sequences can be combined and converted to an appropriate encoding format (e.g., binary), and the combined and converted data can then be returned as a response to the read request.

In some embodiments, data previously encoded via synthesis of biological material may be read in other ways. For example, in some embodiments, if a file corresponding to 4,096 perforation 630 is to be written, rather than identifying 4,096 perforation 630 to write it, the controller may identify 4,096 perforation 630 and then update the index with a number of locations corresponding to the file if those perforations 630 do not form a continuous sequence. As another example, in some embodiments, rather than identifying individual apertures 630, the system controller 120 may group the apertures 630 together (e.g., into groups of 128 apertures 630), thereby reducing the operational costs associated with storing location data (i.e., by reducing the addressing requirement of one address per aperture 630 to one address per group of apertures 630). As another example, in embodiments where data reflecting the location of wells 630 is stored, where DNA strands or other polynucleotides have been synthesized, the data may be stored in various ways, such as sequence identifiers (e.g., well 1, well 2, well 3, etc.) or coordinates (e.g., X and Y coordinates of the well locations in the array).

As another example, in some embodiments, rather than reading the chain 650 from the well 630 in which it was synthesized, the chain 650 may be read from other locations. For example, the chains 650 may be synthesized to include addresses, then cut from the holes 630 and stored in a tube for later retrieval, during which time the included address information may be used to identify the chain 650 corresponding to a particular file. As another illustrative example, the strand 650 may be replicated from the surface using a polymerase, then eluted and stored in a tube. Alternatively, the strand 650 may be replicated onto the beads by using biotinylated oligonucleotides hybridized to DNA strands or other polynucleotides and capturing the extension products on streptavidin beads dispensed in the wells 630. Other examples are possible and will be apparent to those skilled in the art based on this disclosure. Accordingly, the above description of retrieving data encoded by synthesis of biological material should be understood as being merely exemplary and should not be considered as limiting.

Embodiments described herein may use a polymer coating (e.g., a polymer coating described in U.S. patent No. 9,012,022 entitled "polymer coating," published on 21/4 2015, which is incorporated herein by reference in its entirety)) on the surface of the flow cell. Embodiments described herein may utilize one or more labeled nucleotides having a detectable label and a cleavable linker (e.g., those described in U.S. patent No. 7,414,116 entitled "labeled nucleotide chain" published on 8/19 of 2008, which is incorporated herein by reference in its entirety). For example, embodiments described herein may utilize a cleavable linker that can be cleaved by contact with a water-soluble phosphine or a water-soluble transition metal-containing catalyst having a fluorophore as a detectable label. The embodiments described herein can use a dual channel detection method to detect nucleotides of a polynucleotide, such as described in U.S. patent No. 9,453,258 entitled "methods and compositions for nucleic acid sequencing" published 2016, 9, 27, which is incorporated herein by reference in its entirety. For example, embodiments described herein can utilize a fluorescence-based SBS method that has a first nucleotide type detected in a first channel (e.g., dATP with a label detected in the first channel when excited by a first excitation wavelength), a second nucleotide type detected in a second channel (e.g., dCTP with a label detected in the second channel when excited by a second excitation wavelength), a third nucleotide type detected in both the first and second channels (e.g., dTTP with at least one label detected in both channels when excited by the first excitation wavelength and/or the second excitation wavelength), and a fourth nucleotide type that lacks a label that is not detected or only weakly detected in either channel (e.g., dGTP without a label). Embodiments of the cartridges and/or flow cells described herein may be constructed according to one or more teachings described in U.S. patent No. 8,906,320 entitled "biosensor for biological or chemical analysis and system and method thereof" published 12, 9 of 2014 (the entire contents of which are incorporated herein by reference), U.S. patent No. 9,512,422 entitled "gel pattern surface" published 6, 2016 (the entire contents of which are incorporated herein by reference), U.S. patent No. 10,254,225 entitled "biosensor for biological or chemical analysis and method of making the same" published 4, 9, 2019, and/or U.S. patent No. 2018/0117587 entitled "cartridge assembly" published 3, 2018, 5, month 3 (the entire contents of which are incorporated herein by reference).

Use of SBS flow cell for information storage and retrieval and creation of long DNA sequences using SBS flow cell with write function

Because DNA can be used to store a variety of biological and non-biological information, SBS systems and processes can be used to facilitate the writing and reading of DNA-based information to and from flow cells used in such systems and processes. Therefore, it may be beneficial to use SBS systems, devices, and processes to sort and store DNA-based information and use it to retrieve such information when needed.

As previously noted, "machine-written DNA" may be generated to index or otherwise track pre-existing DNA, storing data or information from any other source for any suitable purpose, without intermediate conversion of intermediate data into binary code. As also previously noted, some embodiments utilize sequencing-by-synthesis (SBS) to achieve the read function, although certain aspects of the SBS process can also be used to write certain indexed, classified, or other tissue information into DNA sequences or other polynucleotide sequences. Generally, SBS processes are based on reversible dye terminators that can recognize a single base when introduced into a synthetic polynucleotide. SBS can be used for whole genome and region sequencing, transcriptome analysis, metagenomics, small RNA discovery, methylation analysis, and whole genome protein-nucleic acid interaction analysis. More specifically, SBS sequences tens of millions of clusters on the flow cell surface in a massively parallel fashion using four fluorescently labeled nucleotides. In each sequencing cycle, a single labeled deoxyribonucleoside triphosphate (dNTP) is added to the nucleic acid strand. The nucleotide tag serves as a "reversible terminator" for the polymerization reaction. After incorporation of the dNTPs, the labels (e.g., fluorescent dyes) can be identified by laser excitation and imaging, and then cleaved enzymatically for the next round of incorporation. Base detection (base call) is performed directly from the signal intensity measurement during each cycle. SBS workflows/processes may include the following: (i) preparing a sample; (ii) cluster generation; (iii) sequencing; (iv) and (6) analyzing the data.

In the sample (or library) preparation process, a sequencing library is prepared by fragmentation of a DNA or cDNA sample, which is then extracted and purified. After DNA purification, the first part of the process is "tagging", during which transposase is used to cut the purified DNA into short fragments (which are referred to as inserts or tags). Adapters (5 'and 3') are then ligated to either side of the cleavage site, and the polynucleotides not yet ligated to adapters are washed away. After ligation of the adaptors to the tags, reduced cycling amplification can be used to add other motifs such as sequencing primer binding sites, indices, barcodes and regions complementary to oligonucleotides attached to the flow cell (terminal sequences), as well as other kinds of molecular modifications that serve as reference points during amplification, sequencing and analysis. The index and/or barcode are unique polynucleotide sequences linked to fragments in the sequencing library for downstream computerized classification and identification. During sequence analysis, the computer groups all reads with the same index together. The index is typically a component of an adaptor or PCR primer and is ligated to the library fragments during the sequencing library preparation stage. Such indices are typically between 8-12 bp. Libraries with unique indices can be pooled together, loaded into one lane of a sequencing flow cell, and sequenced in the same run. The reads are then identified and classified using bioinformatics software. This method is called "multiplex".

Clustering is a process in which each DNA fragment is amplified locally in an isothermal manner. During cluster generation, the fragmented DNA library is loaded into a flow cell, which is a slide containing one or more lanes of DNA flowing through. Each lane of the flow cell may be overlaid with two types of surface-bound oligonucleotides (e.g., P5/P7 or P6/P8) complementary to library adaptors, and fragments of the DNA pool captured by these oligonucleotides. Hybridization occurs by the first of the two types of oligonucleotides (e.g., P5 or P6) on the surface. The oligonucleotide is complementary to an adapter region on one of the DNA fragments, thereby binding the DNA fragment. The DNA polymerase is then used to generate the complement of the hybridized DNA fragments. The newly formed double stranded DNA molecules are denatured and the original template is washed away. The remaining polynucleotides are then clonally amplified by a bridge amplification method in which each polynucleotide folds and its adaptor region hybridizes to a second type of oligonucleotide on the flow cell (e.g., P7 or P8). The DNA polymerase is then used to generate the complementary strand, forming a double-stranded bridge. This bridge is then denatured, leaving two single-stranded copies of the molecule tethered (grafted) in the flow cell. The method is then repeated and occurs simultaneously for millions of clusters, resulting in clonal amplification of all fragments in the DNA library. After bridge amplification, the reverse strand is cleaved and washed away, leaving only the positive strand. The 3' ends of these strands are then blocked to prevent unwanted initiation. The clustering process can occur in an automated flow cell instrument or using an onboard cluster generation component within a sequencing instrument. Each cluster can be defined as a clonal grouping of template DNA bound to the surface of the flow cell. As described, each cluster is seeded with a single template polynucleotide and clonally amplified by bridge amplification until the cluster has about 1000 copies. Each cluster on the flow cell generates a single sequencing read. For example, 10,000 clusters on a flow cell can yield 10,000 individual reads and 20,000 paired end reads. After cluster generation is complete, the DNA template is ready for sequencing.

Sequencing begins with extension of a first sequencing primer to generate a first read. In each cycle, four nucleotides (dntps) compete for addition to the growing strand. One or more of the four nucleotides may comprise a label or tag to be identified. Depending on the sequence of the template DNA, only one dNTP can be incorporated per polynucleotide at a time. In some embodiments, after each nucleotide is added, the cluster is excited by a light source and a fluorescent signal is emitted via the label in response to the excitation light source. This method is called sequencing-by-synthesis or SBS. The number of cycles determines the length of the reading. The emission wavelength and signal intensity determine the base detection. For a given cluster, all of the same chains are read simultaneously. Hundreds of millions of clusters are sequenced in a massively parallel method on a flow cell. After the first reading is completed, the read product is rinsed away. In this part of the method, the Index 1(Index 1) read primer is introduced and hybridised to the template. The reads are generated in a manner similar to the first read. After completion of the index read, the read product is washed away and the 3' end of the template is deprotected. The template is then folded and bound to a second oligonucleotide on the flow cell. Index 2 is read in the same manner as index 1. After this part of the method is complete, the index 2 read product is flushed away. The polymerase extends the second flow cell oligonucleotide to form a double-stranded bridge. The double-stranded DNA is linearized and the 3' end is blocked. The original forward strand is cut and washed away, leaving only the reverse strand. Read two begins with the introduction of read two sequencing primers. As with reading a sequence, the sequencing portion of the method is repeated until the desired read length is obtained. The two products read were then washed away. The entire process will yield millions of reads representing all fragments in the sequencing library. Since the sequencing method uses a reversible terminator-based method, which can detect a single base when it is introduced into a DNA template strand, and since all four reversible terminator-bound dntps are present in each sequencing cycle, natural competition can minimize the introduction bias and greatly reduce the original error rate. As a result, highly accurate base-by-base sequencing is achieved, and errors in sequence background specification are almost eliminated even in the repetitive sequence region and the homopolymer.

Some embodiments provide methods of synthesizing nucleic acid sequences up to 2000 base pairs (bp) in length or longer. This synthesis using the polynucleotide writing methods and apparatus described herein writes a single long polynucleotide by simultaneously writing multiple strands of smaller polynucleotides in parallel, and then coupling the strands together using the reverse complement of the parallel smaller polynucleotides. Such long polynucleotides can be used to store large amounts of data, synthesize large genes or other long polynucleotides.

To allow for the synthesis of longer sequences, a plurality of discrete spots (e.g., discrete reaction wells) of the flow cell are used. To write longer DNA strands, a "linker sequence" may be written for two different smaller polynucleotides, allowing the two different smaller polynucleotides to assemble into a larger polynucleotide when one or both of the smaller polynucleotides are extended. In some embodiments, for example for data storage purposes, the linker sequence can be a homopolymer (e.g., a predetermined sequence of single nucleotides (e.g., TTTTTTT)) and a corresponding reverse complement homopolymer (e.g., a predetermined sequence of reverse complement nucleotides (e.g., AAAAAAA)) can be used without affecting the integrity of the written data in the smaller polynucleotide sequence. In embodiments where a predetermined sequence different from the DNA sequence of interest may affect the resulting polynucleotide (e.g., for gene synthesis), the linking sequence may be a sequence (which may be introduced with the homopolymer) that does not introduce non-endogenous or artificial sequences. For example, the linker sequence may be selected as the predetermined nucleotide sequence of the synthetic polynucleotide to be written. That is, for example, if a first written polynucleotide has a corresponding ATCGTGTGACTCGA sequence, a smaller subset of that sequence (e.g., CTCGA) may be selected as a linker sequence, so that the reverse complement sequence (e.g., GAGCT) may be written as part of the sequence of a second polynucleotide, such that the linker sequence does not introduce non-endogenous or artificial sequences into the larger synthetic polynucleotide.

A first polynucleotide comprising a first sequence may be written in a first well or at a first predetermined location of the flow cell and a second polynucleotide comprising a second sequence may be written in a second well or at a second predetermined location of the flow cell. In some embodiments, the first polynucleotide and the second polynucleotide may be written substantially simultaneously, offset in time, and/or at different times. The first polynucleotide and the second polynucleotide may hybridize via the respective first linker sequences. The hybridized first and second polynucleotides may be extended, for example, by a DNA polymerase to produce a strand complementary to each of the first and/or second polynucleotides, thereby producing a third polynucleotide comprising the first and second sequences of the first and second polynucleotides.

A fourth polynucleotide comprising a third sequence can be written in the third well of the flow cell or at a third predetermined location thereof. In some embodiments, the fourth polynucleotide may be written substantially simultaneously, offset in time, and/or at a different time than the first polynucleotide and/or the second polynucleotide. The fourth polynucleotide and the third polynucleotide may hybridize via the respective second linker sequences. The hybridized fourth and third polynucleotides may be extended, for example by a DNA polymerase, to produce a strand complementary to each of the fourth and/or third polynucleotides, thereby producing a fifth polynucleotide comprising the first, second and third sequences of the fourth and third polynucleotides.

The above method can be repeated as an iterative method in which two or more adjacent wells are used to write polynucleotide sequences, the written polynucleotide sequences are hybridized, and the hybridized sequences are extended to construct polynucleotides up to 2000 base pairs or more. These long sequences may represent long genes, minigenomes, or other genetic constructs intended to encode or contain biological or non-biological information. To hybridize a polynucleotide between two or more wells, the gap between the wells can be about 100 nm. In some embodiments, the gap between pores may be greater than 100nm (e.g., 200nm, 300nm, 400nm, 500nm), or the gap between pores may be less than 100nm (e.g., 90nm, 80nm, 70nm, 60nm, 50nm, 40nm, 30nm, 20nm, 10 nm). In this context, an aperture is a reaction chamber having a specific area. In some embodiments, the wells may also correspond to discrete imaged regions, and the wells used for polynucleotides may be used for writing polynucleotides and reading sequences of polynucleotides.

Quality control methods can be performed by reading each polynucleotide prior to hybridization, as described below. During reading and/or writing, "phasing" and/or "predetermined phasing" may occur and introduce errors into the resulting written polynucleotide or read sequence. "phasing" refers to the situation where the reversible terminator of the first incorporated nucleotide is inadvertently removed, e.g., by interaction with residual reagents that have not been washed out of the flow cell, and the second nucleotide is incorporated. During the writing process, this may result in writing two nucleotides for a particular DNA sequence of a polynucleotide, rather than a single nucleotide. During reading this may result in no fluorophore associated with the first nucleotide being detected, thus offsetting the read sequence by skipping one nucleotide. "predetermined phase" refers to the case where no nucleotide is introduced. During the writing process, this may result in no nucleotides being written into the sequence of the polynucleotide. During reading, this may result in no fluorophore associated with a nucleotide of the sequence being detected or a fluorophore associated with a previously detected nucleotide being detected again, thereby deviating the read sequence by delaying or repeating the reading of one nucleotide. Because the synthesis of large base pair polynucleotides (e.g., those greater than 1000 base pairs or greater than 2000 base pairs) can be time consuming, performing quality control methods on smaller polynucleotides that are to be hybridized to form larger base pair polynucleotides can detect errors more quickly during polynucleotide writing, without synthesizing a complete polynucleotide that may contain one or more errors. In some embodiments, the first polynucleotide and/or the second polynucleotide may be sequenced after or during writing, for example by flowing dntps with one or more labels or tags to sequence the written first polynucleotide and/or second polynucleotide or portions thereof. Thus, it can be determined by sequencing-by-synthesis methods whether an error has occurred during writing of the first and/or second polynucleotide prior to hybridizing the first and second polynucleotide together.

During data analysis and alignment, sequences from the pooled sample libraries are isolated based on unique indices introduced during sample preparation. For each sample, reads with similar base detection strings (stretch) were clustered locally. Millions of clusters are sequenced at a time, and each cluster has approximately 1000 copies of the same DNA insert, as previously described. Sequence "reads" generally refer to data strings corresponding to A, T, C and G bases of sample DNA or RNA. Paired forward and reverse reads can create contiguous sequences (called "contigs") that are aligned to a reference genome for variant identification. The reference genome is a fully sequenced and assembled genome, which acts as a scaffold against which new sequences are aligned and compared. The pair end information is used to resolve ambiguous comparisons. After alignment, many variations of analysis are possible, such as Single Nucleotide Polymorphism (SNP) or insertion deletion (indel) recognition, read counting by RNA methods, phylogenetic or metagenomic analysis.

In some embodiments, where barcodes are used to identify or classify library DNA samples or other sample types, the barcodes may be spatial barcodes or non-spatial barcodes. An example of a spatial barcode may be ten different patients generating ten different samples. The barcode of the DNA fragment from patient 1 can be labeled 1, the barcode of the DNA fragment from patient 2 labeled 2, and so on in a discrete fashion until patient 10. In this case, a non-spatial barcode may involve mixing DNA fragments of 10 patients, and then seeding these fragments into a flow cell (which will also be read from) in a random or super-random format. Spatial barcode may also refer to the positioning of a library sample on a flow cell where each DNA fragment from patient 1 (or from the same source) is located on a highly localized spatially predefined region (e.g., channel) on the flow cell. Retrieval of a particular barcode may then be used to identify a particular region of the flow cell from which data is retrieved. Such a bar code is basically a grouping or cataloging method that can be used for a variety of purposes. It is known that such barcoding or indexing methods can be used to reassemble previously written sequences, and that essentially any type of data can be spatially encoded in this manner. For example, spatial barcodes or spatial writing of certain information can be used to reconstruct long genes or to reconstruct genomes, where the spatial arrangement or location of small DNA fragments will drive the self-assembly of genomes or the assembly of very long gene fragments.

The unknown information is not typically extracted from the index or barcode, but rather the index and barcode are used to assign labels uni-directionally to a particular pool of clusters. The initial primers immobilized on the flow cell may also comprise barcode sequences. For example, a primer sequence may comprise a fixed barcode or random sequence that generates a unique molecular index that can be used to track or locate data stored as a sequence.

Barcodes (indexes) may also be used to improve retrieval of stored data. For example, when writing data, a barcode location may be allocated for tracking. The barcode may be inserted at predetermined intervals during the process of writing. For example, after initial library inoculation and amplification, selected nucleotides can be sequentially introduced into the flow cell to introduce non-native sequences that serve as barcodes. The barcode may further be used to indicate the location of a DNA strand "match" during reading and may be aligned to decode the data stored as a sequence.

Information can also be written to or read from the flow cell using a real-time sample index. This type of indexing involves writing a known or specific sequence on the flow cell for various organizational purposes or other functions. Referring to fig. 11, a "capture probe" is created by writing a sequence of interest on a flow cell. The sequence of interest may represent a particular exon or amplicon that is closely associated with a particular disease or a particular biological problem. A number of thymines (poly T) may be added to the P5 primer that has been grafted onto the flow cell so that mRNA having an adenine (A) tail flowing into the flow cell will hybridize to the capture probe. After this binding event has occurred, cDNA synthesis can be used to copy the specific region (or region of interest) that binds to the flow cell. P7' primers can be added to the end of each binding sequence to complete the preparation of the sample library. The method of preparing a sample library, capturing the library of interest, and then ligating adaptors to the captured library sequences is referred to as "writing down" sequences. Ligation of adaptors will create clusters that will generate the desired complexes. Referring to fig. 11, a P7' adaptor is typically ligated to the unbound end of the captured library molecule, and at this ligation portion of the process, additional sequence data may be written onto the captured strand. In essence, this method adds both P5 and P7 simultaneously during the creation of the sample library, so that the library DNA fragments can be manipulated on the flow cell prior to clonal amplification, an important component of the SBS method.

Fig. 12 depicts another method for storing biological information on a flow cell. In this figure, unique or different indices or barcodes are arranged and written in a predetermined spatial pattern over a flow cell (e.g., pre-assigned pixels). The indices or barcodes may be of known sequence, or they may be randomly generated oligonucleotides. Each index or barcode is used to capture DNA molecules from a different portion of the tissue sample, and each pixel records a very localized capture event that can be read from the flow cell. The term spatial transcriptomics may be used to describe this approach because there are different expression patterns throughout the tissue, or, for example, the location of RNAs located in different parts of the cell (e.g., long neuronal cells) that provide different information about the function and presence status of the cell.

Referring to fig. 13, data storage and retrieval using SBS flow cells or the like may involve the use of certain molecular security measures, which are particularly important when the information of interest includes patient data. As shown in fig. 13, a particular sequence is anchored to a particular pixel or tile on the flow cell, and then molecules or nanoparticles (e.g., "magic ink") are attached to the sequence to create an optical or digital signature that can only be decrypted with a known key. Data stored in the flowpool cannot be accessed without a signature or specific "key" for accessing the data.

FIG. 14 depicts another method of sample indexing on a flow cell. In this method, a flow cell with primers P5 and P7 is provided. The P5 primer has the following sequence: 5'-AATGATACGGCGACCGA-3', the P7 primer has the following sequence: 5'-CAAGCAGAAGACGGCATACGAGAT-3' are provided. Round 1 of the method involves seeding the library on the P5 primer, extending the library sequences, and then writing adenine (a) on the unbound end of each sequence. Round 2 of the method involved inoculating a second batch of libraries on the primers, extending the library sequences, then writing thymine (T) on the end of each new sequence and writing it on the end of each sequence that had been written to a before. This process was continued using cytosine (C) and guanine (G) in sequence until a fully indexed library was created as shown. Finally, the P7' sequence was written at the end of each sequence to allow for cluster generation.

Regarding the use of the P5/P7 primer and the P6/P8 primer, simultaneous manipulation of the two different types of primer sets allows an exponential increase in the copy number of the molecule of interest. The use of two primer sets allows the creation of two different libraries, thereby creating two different types of clusters on the flow cell. This approach allows more information to be obtained from a single pixel and a single flow cell. FIG. 15 depicts a method of using P5/P7 primer and P6/P8 primer on a single flow cell. In preparing the flow cell, a flow cell having both reaction wells and interstitial spaces between the wells is provided. Each reaction well contains PAZAM polymer and the interstitial spaces have been silanized or otherwise pretreated. Then, the initiator primer was inoculated to the silanized gap region, and then the P6/P8 primer was written thereto. Next, the P5/P7 primer was grafted into the reaction well. Next, the sample library was inoculated onto both sets of primer pairs. The P5/P7 sequences were linearized to read the clusters that occurred in the reaction wells, and the P6/P8 sequences were linearized to read the clusters that occurred in the gap regions, allowing for differentiation of the data based on the primer set used.

FIG. 16 depicts another method of sample indexing on a flow cell using the attachment of adjacent molecules. In this method, a flow cell with primers P5 and P7 is provided. The first part of the method involves seeding a P5' library, amplifying the sequences and writing adenine (a) on the unbound end of each sequence. The second part of the method involves seeding a P7' library, amplifying the sequences and writing a thymine (T)/adenine (a) -TATAT sequence on the unbound end of each sequence. In step (iii), AMSI extension is performed after ligation hybridization. Two adjacent libraries were ligated to form a compound library with both P5-P7 'and P7-P5' for clustering. Other sequences may be used if adjacent DNA molecules have complementary sequences. For example, one sequence may be ATGAGCTA and the reverse complement may be taggctcat.

FIG. 17 provides a map of a polynucleotide, e.g., a DNA molecule, synthesized according to the foregoing method embodiments. In the particular embodiment shown, the linker sequence of homopolymer a is written for the first polynucleotide (with P5 as a root) and the reverse complement linker sequence of homopolymer T is written for the second polynucleotide (with P7 as a root). The first polynucleotide and the second polynucleotide can then be hybridized together using the linker sequence and the reverse complementary linker sequence. In some embodiments, e.g., for data storage in polynucleotides, homopolymers may be omitted during readout and/or may be used to check whether errors have occurred during readout. That is, for example, if a polynucleotide written before the homopolymer has a predetermined length (e.g., 150 base pairs) and the resulting sequencing encounters the homopolymer after 149 base pairs or less or after 151 base pairs or more, an error can be detected and a new read-out method can be implemented to re-read the data and/or otherwise mitigate (e.g., by utilizing a mirrored polynucleotide chain from a spare well).

While homopolymers may be used in data storage or other embodiments where non-endogenous or artificial sequences do not affect the resulting polynucleotide, in other embodiments (e.g., gene synthesis), such non-endogenous or artificial sequences may alter or render the resulting polynucleotide ineffective for the intended purpose. Thus, the connecting sequence may alternatively be a subset of the sequence to be written for both the first and second polynucleotides. I.e., the joining sequence will be a complementary sequence to a portion of the polynucleotide that is already the gene being generated. Applications of this embodiment include: (i) creating long DNA fragments as an analysis or calibration tool; (ii) writing a set of long catch-all oligonucleotides hundreds of bases long for pathogen screening panels (panel) to detect pathogens from blood samples; (iii) custom panels are quickly made to read the incoming pathogen and treatment protocols are created using DNA-based vaccines or spontaneous transformation (RNA replication from DNA) that can be used to interfere with the function of the pathogen in vivo. In other words, this embodiment may provide a screening/diagnostic tool that may also become a rapid treatment tool. In fig. 17, the P5 primer has the following sequence: 5'-AATGATACGGCGACCGA-3', and the P7 primer has the following sequence: 5'-CAAGCAGAAGACGGCATACGAGAT-3' are provided.

When sequencing, such as using a CMOS sequencing chip with photodiodes, or using an objective lens with an image sensor with photodiodes, image correction techniques (e.g., correcting for image optical or spectral crosstalk between different pixels), streak distortion, geometric distortion, and/or other errors of the objective lens may be implemented. The calibration method may vary from one chip to another and/or from one instrument to another. One embodiment of the polynucleotide synthesis methods described herein is the generation of a spatially controlled training data set on a flow cell with diversity for base call training data, in particular for optical systems. That is, groups on a flow cell of known polynucleotide sequence can be written in different wells so that the resulting sequences are all known. Thus, when performing the reading method, using a CMOS chip with a photodiode or an image sensor with an objective lens, the raw output data generated by the CMOS chip and/or the image sensor can be calibrated and/or corresponding image corrections can be determined from known different sequences at different well locations. For example, a smaller pitch flow cell may have distortions near each well that can be corrected for based on the known calibration sequence of the polynucleotide on the flow cell. The calibration method may include an on-board quality control system based on writing a plurality of predetermined sequences of polynucleotides on a calibration flow cell. The method may provide individual pixel crosstalk correction and/or imaging patch correction based on the creation of known truth values or truth tables. Known sequences can be written at predetermined spaces on the flow cell to synchronize the sequencer and/or possible random access. The method may also allow for in-situ calibration (e.g., a predetermined sequence may be written at multiple holes and then sequenced, and correction coefficients may be calculated based on any determined error between the read sequence and/or raw data and a known predetermined sequence).

VIII. other

All references, including patents, patent applications, and articles, are incorporated by reference herein in their entirety.

The previous description is provided to enable any person skilled in the art to practice the various configurations described herein. While the subject technology has been described in detail with reference to various figures and configurations, it is to be understood that these are for purposes of illustration only and are not to be construed as limiting the scope of the subject technology.

All applications, patents, and publications (including appendices) mentioned in this application are incorporated by reference in their entirety.

As used herein, an element or step recited in the singular and proceeded with the word "a" or "an" should be understood as not excluding plural said elements or steps, unless such exclusion is explicitly recited to the contrary. Furthermore, references to "one embodiment" are not intended to be interpreted as excluding the existence of additional embodiments that also incorporate the recited features. Furthermore, unless explicitly stated to the contrary, embodiments "comprising" or "having" an element or a plurality of elements having a particular property may include additional elements whether or not they have that property.

The terms "substantially" and "approximately" are used throughout the specification to describe and explain small fluctuations, such as fluctuations due to variations in processing. For example, they may refer to less than or equal to ± 5%, such as less than or equal to ± 2%, such as less than or equal to ± 1%, such as less than or equal to ± 0.5%, such as less than or equal to ± 0.2%, such as less than or equal to ± 0.1%, such as less than or equal to ± 0.05%.

There are many other ways to implement the subject technology. The various functions and elements described herein may be divided differently than shown without departing from the scope of the subject technology. Various modifications to these embodiments will be readily apparent to those skilled in the art, and the generic principles defined herein may be applied to other embodiments. Accordingly, many changes and modifications may be made to the present technology by one of ordinary skill in the art without departing from the scope of the present technology. For example, a different number of given modules or units may be employed, a different type of given modules or units may be employed, given modules or units may be added, or given modules or units may be omitted.

Underlined and/or italicized headings and subheadings are used for convenience only, do not limit the subject technology, and are not mentioned in explaining the subject technology. All structural and functional equivalents to the elements of the various embodiments described throughout this disclosure that are known or later come to be known to those of ordinary skill in the art are expressly incorporated herein by reference and are intended to be encompassed by the subject technology. Moreover, nothing disclosed herein is intended to be dedicated to the public regardless of whether such disclosure is explicitly recited in the above description.

It should be understood that all combinations of the foregoing concepts and other concepts discussed in greater detail below (provided that such concepts do not contradict each other) are considered a part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are considered part of the inventive subject matter disclosed herein.

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System and method for information storage and retrieval using flow cells

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