Compositions and methods for nucleic acid sequencing

• US 8,153,375 B2
• Filed: 03/27/2009
• Issued: 04/10/2012
• 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 W
• Application Number:
  US12/413,258
• Publication Number:
  US 20090298075A1
• Time in Patent Office: 1,110 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/183, 435/6.1, 435/6.11, 435/6.12, 436/94, 436/501, 536/23.1, 536/24.3, 536/24.33, 536/25.3
• US Class Current: 435/6.12
• 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 determining a nucleotide sequence of a template nucleic acid segment, comprising:

providing a contiguous nucleic acid molecule comprising a sense strand and an antisense strand of the template nucleic acid segment, wherein the sense strand and the antisense strand are complementary to each other, the sense strand and the antisense strand are completely contiguous;

sequencing both the sense and antisense strands in a polymerase mediated, template dependent sequencing process; and

determining a sequence of the template nucleic acid segment by comparing sequencing data from each of the sense and antisense strands.

2. The method of claim 1, wherein the sense and antisense strands are linked at each end by first and second linking oligonucleotides, respectively.

3. The method of claim 1, wherein said sequencing both the sense and antisense strands comprises sequencing at least one of the sense and antisense strands more than once.

4. The method of claim 1, wherein said sequencing both the sense and antisense strands comprises contacting the contiguous nucleic acid molecule with a primer sequence that is complementary to at least a portion of the first linking oligonucleotide.

5. The method of claim 1, wherein said sequencing both the sense and antisense strands comprises sequencing the template nucleic acid segment more than once.

6. The method of claim 1, wherein said sequencing both the sense and antisense strands comprises sequencing the template nucleic acid segment more than twice.

7. The method of claim 1, wherein the polymerase mediated, template dependent sequencing process comprises detecting incorporation of each nucleotide incorporated by the polymerase mediated, template dependent sequencing process.

8. The method of claim 7, wherein said detecting incorporation comprises detecting incorporation of each nucleotide incorporated by an individual polymerase in the polymerase mediated, template dependent sequencing process.

9. A method of sequencing a template nucleic acid segment, comprising:

providing a template nucleic acid segment comprising;

a sense nucleic acid strand and an antisense nucleic acid strand that are complementary to each other;

a first connecting nucleic acid linking a 3′

end of the sense nucleic acid strand to a 5′

end of the antisense nucleic acid strand; and

a second connecting nucleic acid linking a 5′

end of the sense nucleic acid strand to a 3′

end of the antisense nucleic acid strand;

contacting the template nucleic acid segment with a primer sequence complementary to at least a portion of the template nucleic acid segment;

monitoring a sequencing process of a template directed, polymerase mediated nucleic acid sequencing of the template nucleic acid segment, thereby determining nucleotide sequencing data from each of the sense and antisense nucleic acid strands of the template nucleic acid segment; and

determining a sequence of the template nucleic acid segment by comparing said sequencing data from each of the sense and antisense nucleic acid strands.

10. The method of claim 9, wherein the sequencing process sequences at least one of the sense and antisense nucleic acid strands of the template nucleic acid segment more than once.

11. The method of claim 9, wherein the sequencing process sequences both the sense and antisense nucleic acid strands of the template nucleic acid segment more than once.

12. The method of claim 11, wherein at least one of the first connecting nucleic acid and the second connecting nucleic acid is a hairpin oligonucleotide.

13. The method of claim 9, further comprising:

providing a double stranded nucleic acid comprising the sense and antisense nucleic acid strands bound together in the double stranded nucleic acid;

linking the first connecting nucleic acid to the 3′

end of the sense nucleic acid strand and the 5′

end of the antisense nucleic acid strand;

linking the second connecting nucleic acid to the 3′

end of the antisense nucleic acid strand and the 5′

end of the sense nucleic acid strand; and

thereby forming the template nucleic acid segment, wherein a primer recognition sequence is within at least one of the first and second connecting nucleic acids.