Methods and compositions for isolating nucleic acid sequence variants

• US 7,635,566 B2
• Filed: 06/27/2008
• Issued: 12/22/2009
• Est. Priority Date: 06/29/2007
• Status: Active Grant

• Current Assignee: Agency For Science Technology and Research (Government of Singapore)
• Original Assignee: Population Genetics Technologies Ltd.
• Inventors: Brenner, Sydney
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US12/163,571
• Publication Number:
  US 20090004665A1
• Time in Patent Office: 543 Days
• Field of Search: 435/6, 536/22.1, 536/23.1, 536/24.3
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

The invention is drawn to isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. The nucleic acids analyzed are generally single stranded and have a reference sequence which is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer. The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analyzed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analyzed does not match the reference sequence. Nucleic acid strands that have mutations can be isolated using a variety of methods and sequenced to determine the precise identity of the mutation/polymorphism. By performing the method on both strands of the nucleic acid being analyzed, virtually all possible mutations can be identified.

Claims

1. A method of sorting nucleic acid molecules according to the identity of their corresponding unique nucleotide tags, said method comprising:

(i) contacting a nucleic acid sample comprising at least two nucleic acid molecules each having a unique tag to a capture primer under hybridization conditions, wherein said capture primer is immobilized on a substrate and comprises a sequence complementary to a capture primer binding site in said at least two nucleic acid molecules, whereby said at least two nucleic acid molecules are immobilized;

(ii) contacting said immobilized at least two nucleic acid molecules to a polymerization primer under hybridization conditions, wherein said polymerization primer comprises a sequence complementary to all of or a region in the unique tag of a first of said at least two nucleic acid molecules, wherein said polymerization primer binds to the same strand of said first nucleic acid molecules as said capture primer at a location that is 5′

to said capture primer; and

(iii) isolating said first nucleic acid molecules by contacting said immobilized at least two nucleic acid molecules to a displacing nucleotide polymerase under nucleic acid polymerization conditions, wherein extension of said polymerization primer displaces said first nucleic acid molecules from said immobilized capture primer;

wherein said at least two uniquely-tagged nucleic acid molecules are sorted according to the identity of their corresponding unique nucleotide tags.

2. The method of claim 1, wherein said method further comprises isolating a second of said at least two nucleic acid molecules by repeating steps (ii) and (iii) using a second polymerization primer, wherein said second polymerization primer comprises a sequence complementary to all of or a region in the unique tag of said second nucleic acid molecules, wherein said second polymerization primer binds to the same strand of said second nucleic acid molecules as said capture primer at a location that is 5′

to said capture primer.

3. The method of claim 1, wherein said substrate is a pin.

4. The method of claim 1, wherein said capture primer is immobilized on said substrate via interaction between a binding moiety on said capture primer and a binding partner specific for said binding moiety on said substrate.

5. The method of claim 4, wherein said binding moiety is biotin.

6. The method of claim 1, wherein said at least two nucleic acid molecules have different origins.

7. The method of claim 6, wherein said unique tag denotes the origin of each of said at least two nucleic acid molecules.

8. The method of claim 1, wherein said unique tag of said at least two nucleic acid molecules comprises multiple distinct regions, wherein said multiple distinct regions are non-cross hybridizing regions.

9. The method of claim 8, wherein each of said multiple distinct regions comprises a sequence token tag.

10. The method of claim 8, wherein said isolated first nucleic acid molecules of step (iii) are subjected to a second round of sorting according to the identity of a second of said multiple distinct regions in said unique tag.

11. The method of claim 10, wherein the polymerization primer employed in step (ii) for the first round of sorting comprises a binding moiety, wherein step (i) of the second round of sorting comprises contacting the isolated first nucleic acid molecules of step (iii) in the first round of sorting to a second substrate having immobilized thereon corresponding binding partners of said binding moiety to immobilize said isolated first nucleic acid molecules, thereby converting the polymerization primer in the first round of sorting to the capture primer in the second round of sorting.

12. The method of claim 8, wherein said isolated first nucleic acid molecules of step (iii) are subjected to iterative rounds of sorting according to the identity of each of said multiple distinct regions in said unique tag.

13. The method of claim 12, wherein the polymerization primer employed in step (ii) for a prior round of sorting comprises a binding moiety, wherein step (i) in the subsequent round of sorting comprises contacting the isolated nucleic acid molecules of step (iii) in the prior round of sorting to a substrate having immobilized thereon corresponding binding partners of said binding moiety to immobilize said isolated nucleic acid molecules, thereby converting the polymerization primer in a prior round of sorting to the capture primer in a subsequent round of sorting.

14. The method of claim 8, wherein said capture primer is specific for a first of said multiple distinct regions in said unique tag.

15. The method of claim 8, wherein step (i) further comprises employing multiple capture primers immobilized on separate substrates, wherein each of said multiple capture primers is specific for a corresponding first of said multiple distinct regions in said at least two nucleic acid molecules.

16. The method of claim 15, wherein the polymerization primer employed in step (ii) is identical for each of said multiple capture primers.

17. The method of claim 15, wherein said multiple capture primers are immobilized on different pins of a comb.

18. The method of claim 15, wherein said multiple capture primers are immobilized on different pins of a brush.

19. A method of sorting nucleic acid molecules according to the presence of a unique nucleotide sequence, said method comprising:

(i) contacting a nucleic acid sample comprising at least two nucleic acid molecules to a capture primer under hybridization conditions, wherein said capture primer is immobilized on a substrate and comprises a sequence complementary to a capture primer binding site present in said at least two nucleic acid molecules, whereby said at least two nucleic acid molecules are immobilized;

(ii) contacting said immobilized at least two nucleic acid molecules to a polymerization primer under hybridization conditions, wherein said polymerization primer comprises a sequence complementary to a unique sequence present in a first of said at least two nucleic acid molecules, wherein said polymerization primer binds to the same strand of said first nucleic acid molecules as said capture primer at a location that is 5′

to said capture primer; and

(iii) isolating said first nucleic acid molecules by contacting said immobilized at least two nucleic acid molecules to a displacing nucleotide polymerase under nucleic acid polymerization conditions, wherein extension of said polymerization primer displaces said first nucleic acid molecules from said immobilized capture primer;

wherein said nucleic acid molecules are sorted according to the presence of said unique sequence.

20. The method of claim 19, wherein said method further comprises isolating a second of said at least two nucleic acid molecules by repeating steps (ii) and (iii) using a second polymerization primer, wherein said second polymerization primer comprises a sequence complementary to a second unique sequence present in said second nucleic acid molecules, wherein said second polymerization primer binds to the same strand of said second nucleic acid molecules as said capture primer at a location that is 5′

to said capture primer.