Methods and compositions for isolating nucleic acid sequence variants

• US 8,241,850 B2
• Filed: 11/09/2009
• Issued: 08/14/2012
• Est. Priority Date: 06/29/2007
• Status: Active Grant

• Current Assignee: Agency For Science Technology and Research
• Original Assignee: Population Genetics Technologies Ltd.
• Inventors: Brenner, Sydney
• Primary Examiner(s): Whisenant, Ethan C
• Application Number:
  US12/615,051
• Publication Number:
  US 20100136557A1
• Time in Patent Office: 1,009 Days
• Field of Search: 435/6.1, 435/91.2, 536/23.1, 536/24.3
• US Class Current: 435/6.1
• 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 eluting a polynucleotide from a capture primer, comprising:

using a strand displacing nucleic acid polymerase to initiate nucleic acid synthesis on a polynucleotide hybridized to a capture primer via a capture primer binding site in the polynucleotide, wherein nucleic acid synthesis is initiated upstream of the capture primer binding site on the polynucleotide and proceeds through the capture primer binding site, thereby eluting the polynucleotide from the capture primer

wherein the method comprises sorting a mixture of differentially tagged polynucleotides according the identity of their respective nucleic acid tags.

2. The method of claim 1, wherein the capture primer is immobilized on a substrate.

3. The method of claim 1, wherein nucleic acid synthesis is initiated from a polymerization primer hybridized to a polymerization primer binding site in the polynucleotide.

4. The method of claim 3, wherein the capture primer binding site and/or the polymerization primer binding site are present in a first and/or a second adapter region of the polynucleotide.

5. The method according to claim 4, wherein the capture primer binding site and/or the polymerization primer binding site includes all or part of a nucleic acid tag in the first and/or second adapter region of the polynucleotide.

6. The method of claim 3, wherein the method is drawn to sorting a mixture of polynucleotides based on whether a polynucleotide in the mixture hybridizes to the capture primer, hybridizes to the polymerization primer, and/or initiates and support nucleic acid synthesis from a hybridized polymerization primer through the capture primer binding site.

7. A method of sorting a mixture of differentially tagged nucleic acid molecules according to the identity of their corresponding nucleotide tags, the method comprising:

(i) contacting a nucleic acid sample comprising a mixture of differentially tagged nucleic acid molecules to a capture primer under hybridization conditions, wherein the capture primer is immobilized on a substrate and comprises a sequence complementary to a capture primer binding site in each of the differentially tagged nucleic acid molecules, whereby the differentially tagged nucleic acid molecules are immobilized;

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

to the capture primer; and

(iii) isolating the one or more first nucleic acid molecules by contacting the immobilized differentially tagged nucleic acid molecules to a displacing nucleotide polymerase under nucleic acid polymerization conditions, wherein extension of the polymerization primer displaces the one or more first nucleic acid molecules from the immobilized capture primer;

wherein the mixture of differentially tagged nucleic acid molecules are sorted according to the identity of their corresponding nucleotide tags.

8. The method of claim 7, wherein the method further comprises isolating one or more second nucleic acid molecules by repeating steps (ii) and (iii) using a second polymerization primer, wherein the second polymerization primer comprises a sequence complementary to all of or a region in the unique tag of the one or more second nucleic acid molecules, wherein the second polymerization primer binds to the same strand of the second nucleic acid molecules as the capture primer at a location that is 5′

to the capture primer.

9. The method of claim 8, wherein the one or more first nucleic acid molecules and the one or more second nucleic acid molecules are derived from different nucleic acid sources denoted by their respective differential tags.

10. The method of claim 7, wherein the tag of each of the differentially tagged nucleic acid molecules comprises multiple distinct regions, and wherein the isolated one or more first nucleic acid molecules are subjected to a second round of sorting according to the identity of a second of the multiple distinct regions in the 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 the binding moiety to immobilize the 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 10, wherein the capture primer used in step (i) is specific for one of the multiple distinct regions in the tag of the differentially tagged nucleic acid molecules.

13. The method of claim 12, wherein step (i) further comprises employing multiple capture primers immobilized on separate substrates, wherein each of the multiple capture primers is specific for a corresponding first of the multiple distinct regions in the differentially tagged nucleic acid molecules.

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

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

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

to the capture primer; and

(iii) isolating the one or more first nucleic acid molecules by contacting the immobilized nucleic acid molecules to a strand displacing nucleotide polymerase under nucleic acid polymerization conditions, wherein extension of the polymerization primer displaces the one or more first nucleic acid molecules from the immobilized capture primer;

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

15. The method of claim 14, wherein the method further comprises isolating one or more second nucleic acid molecules is the mixture by repeating steps (ii) and (iii) using a second polymerization primer, wherein the second polymerization primer comprises a sequence complementary to a second unique sequence present in the one or more second nucleic acid molecules, wherein the second polymerization primer binds to the same strand of the one or more second nucleic acid molecules as the capture primer at a location that is 5′

to the capture primer.