Compositions and methods for nucleic acid sequencing

• US 9,404,146 B2
• Filed: 04/19/2013
• Issued: 08/02/2016
• Est. Priority Date: 03/28/2008
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Travers, Kevin, Otto, Geoff, Turner, Stephen, Heiner, Cheryl, Ma, Congcong
• Primary Examiner(s): Lu, Frank
• Application Number:
  US13/866,603
• Publication Number:
  US 20130309678A1
• Time in Patent Office: 1,201 Days
• Field of Search: 435/6.1, 435/6.11, 435/6.12, 435/91.1, 435/91.2, 435/183, 436/94, 436/501, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/25.32
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.

Claims

1. A method of sequencing nucleic acid molecules with improved accuracy, comprising:

providing said nucleic acid molecules, each of said nucleic acid molecules comprising a double-stranded portion, the double-stranded portion consisting of a forward strand and a reverse strand, wherein the forward strand and the reverse strand are fully complementary to each other;

linking a 3′

end of the forward strand to a 5′

end of the reverse strand of each of said nucleic acid molecules, thereby forming a plurality of template molecules, wherein said 3′

end of the forward strand and said 5′

end of the reverse strand are linked by a linking oligonucleotide;

performing at least one single-molecule sequencing process on each of said plurality of template molecules, wherein the forward strand and the reverse strand in each of said plurality of template molecules are fully complementary to each other, each of said at least one single-molecule sequencing process consisting of sequencing only one single template molecule of said plurality of template molecules, thereby generating a sequence read from each of said plurality of template molecules, said sequence read comprising sequences of both the forward strand and the reverse strand of each of said plurality of template molecules; and

determining the sequence of each of said plurality of template molecules by analyzing said sequence read from each of said plurality of template molecules, including comparing the sequences of the forward strand and the reverse strand from each of said plurality of template molecules, thereby improving sequencing accuracy of said nucleic acid molecules.

2. The method of claim 1, further comprising linking a 5′

end of the forward strand to a 3′

end of the reverse strand, wherein said 5′

end of the forward strand and said 3′

end of the reverse strand are linked by a second linking oligonucleotide, wherein said linking a 5′

end of the forward strand to a 3′

end of the reverse strand occurs prior to said performing at least one single-molecule sequencing process.

3. The method of claim 1, wherein said at least one single-molecule sequencing process comprises contacting each of said plurality of template molecules with a primer sequence that is complementary to a single-stranded portion of said plurality of template molecules.

4. The method of claim 1, wherein said at least one single-molecule sequencing process comprises initiating sequencing at a gap within each of said plurality of template molecules.

5. The method of claim 1, wherein said at least one single-molecule sequencing process includes single-molecule sequencing of the linking oligonucleotide.

6. The method of claim 1, wherein said at least one single-molecule sequencing process is performed using an electrochemical system.

7. The method of claim 1, wherein said at least one single-molecule sequencing process is performed using a nanopore sensor.

8. The method of claim 1, wherein said at least one single-molecule sequencing process is performed using a sequencing by synthesis technology.

9. The method of claim 8, wherein said sequencing synthesis technology comprises detecting incorporation of each nucleotide incorporated by a polymerase mediated, template dependent sequencing process during said at least one single-molecule sequencing process.

10. The method of claim 1, wherein said double-stranded portion comprises at least 500 base pairs.

11. The method of claim 1, wherein said, linking oligonucleotide comprises a registration sequence.

12. The method of claim 1, wherein each of said nucleic acid molecules further comprises a single-stranded portion.

13. The method of claim 1, wherein each of said nucleic acid molecules further comprises an overhang region and said linking a 3′

end of the forward strand to a 5′

end of the reverse strand of each of said nucleic acid molecules comprises ligating said linking oligonucleotide to said overhang region on each of said nucleic acid molecules.

14. A method of generating nucleotide sequence data for nucleic acid sequencing template molecules, comprising:

providing said nucleic acid sequencing template molecules, each of said nucleic acid sequencing template molecules consisting of;

two nucleic acid strands that are fully complementary to each other and are linked at their one end by a connecting nucleic acid that links a 3′

end of one strand of the two nucleic acid strands to a 5′

end of another strand of the two nucleic acid strands;

performing at least one single-molecule sequencing process on each of said nucleic acid sequencing template molecules, each of said at least one single-molecule sequencing process consisting of sequencing only one single template molecule of said nucleic acid sequencing template molecules; and

monitoring said at least one single molecule sequencing process, thereby generating nucleotide sequence data for each of said two nucleic acid strands of each of said nucleic acid sequencing template molecules, and

comparing the sequence data of the two nucleic acid strands from the same nucleic acid template molecule of said nucleic acid sequencing template molecules.

15. The method of claim 14, wherein said at least one single-molecule sequencing process is performed using a sequencing by synthesis technology.

16. The method of claim 14, wherein said at least one single-molecule sequencing process is performed using an electrochemical system.

17. The method of claim 14, wherein said at least one single-molecule sequencing process is performed using a nanopore sensor.

18. The method of claim 14, further comprising comparing the nucleotide sequence data of said one strand of the two nucleic acid strands to the nucleotide sequence data of said another strand of the two nucleic acid strands to determine a nucleotide sequence of each of the nucleic acid sequencing templates.

19. The method of claim 14, wherein said connecting nucleic acid is a hairpin or stem-loop oligonucleotide.

20. A method of sequencing a linear, single nucleic acid template with improved accuracy, comprising:

providing a nucleic acid molecule comprising a double-stranded nucleic acid segment consisting of a first strand and a second strand, wherein the first strand and the second strand are fully complementary to each other;

ligating a linking oligonucleotide to a 3′

end of said first strand and a 5′

end of said second strand, wherein the linking oligonucleotide connects said first strand to said second strand of said double-stranded nucleic acid segment, thereby forming a linear, single-stranded nucleic acid sequencing template molecule comprising both said first strand and said second strand, wherein the first strand and the second strand of said linear, single-stranded nucleic acid sequencing template molecule are fully complementary to each other;

performing single-molecule sequencing of said linear, single-stranded nucleic acid sequencing template molecule, said single-molecule sequencing consisting of sequencing only one single template molecule of said linear, single-stranded nucleic acid sequencing template molecule, thereby obtaining a sequence read for said linear, single-stranded nucleic acid sequencing template molecule, wherein said sequence read comprises sequences of said first strand and said second strand of said double-stranded nucleic acid segment, and

determining a sequence of the nucleic acid segment by analyzing said sequencing read, including comparing the sequences of said first strand and said second strand from said linear, single-stranded nucleic acid sequencing template molecule, thereby improving sequencing accuracy of said linear, single-stranded nucleic acid sequencing template molecule.

21. The method of claim 20, wherein said performing single-molecule sequencing of said linear, single-stranded nucleic acid sequencing template molecule comprises sequentially detecting nucleotides in said linear, single-stranded nucleic acid sequencing template molecule.

22. The method of claim 21, wherein said sequentially detecting nucleotides is performed using a polymerase mediated template directed sequencing process.

23. The method of claim 21, wherein said sequentially detecting nucleotides is performed using an electrochemical system.

24. The method of claim 21, wherein said sequentially detecting nucleotides is performed using a nanopore sensor.

25. The method of claim 20, wherein said double-stranded nucleic acid segment comprises at least 500 base pairs.

26. The method of claim 20, wherein said linking oligonucleotide comprises a registration sequence.

27. The method of claim 20, wherein said nucleic acid molecule further comprises an overhang region and said ligating a linking oligonucleotide to a 3′

end of said first strand and a 5′

end of said second strand comprises ligating said linking oligonucleotide to said overhang region on said nucleic acid molecule.