Serial coupling of nucleic acid metabolism and extension for nucleic acid amplification

• US 7,919,253 B2
• Filed: 11/04/2009
• Issued: 04/05/2011
• Est. Priority Date: 02/23/2000
• Status: Expired due to Fees

• Current Assignee: City of Hope
• Original Assignee: City of Hope
• Inventors: Sommer, Steve S., Liu, Qiang
• Primary Examiner(s): Horlick; Kenneth R.
• Application Number:
  US12/612,162
• Publication Number:
  US 20100129871A1
• Time in Patent Office: 517 Days
• Field of Search: 435/6, 435/91.1, 435/91.2
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)

Abstract

A novel method of pyrophosphorolysis activated polymerization (PAP) has been developed. In PAP, pyrophosphorolysis and polymerization by DNA polymerase are coupled serially for each amplification by using an activatable oligonucleotide P* that has a non-extendible 3′-deoxynucleotide at its 3′ terminus. PAP can be applied for exponential amplification or for linear amplification. PAP can be applied to amplification of a rare allele in admixture with one or more wild-type alleles by using an activatable oligonucleotide P* that is an exact match at its 3′ end for the rare allele but has a mismatch at or near its 3′ terminus for the wild-type allele. PAP is inhibited by a mismatch in the 3′ specific sequence as far as 16 nucleotides away from the 3′ terminus. PAP can greatly increase the specificity of detection of an extremely rare mutant allele in the presence of the wild-type allele. Specificity results from both pyrophosphorolysis and polymerization since significant nonspecific amplification requires the combination of mismatch pyrophosphorolysis and misincorporation by the DNA polymerase, an extremely rare event. Using genetically engineered DNA polymerases greatly improves the efficiency of PAP.

Claims

1. A process which comprises serial coupling of two reactions, the first reaction being activation of an inactive oligonucleotide which, if not activated, would prevent the oligonucleotide from being extended on a nucleic acid template and the second reaction being an extension of the activated oligonucleotide on the nucleic acid template, wherein the inactive oligonucleotide has a match at the 3′

end nucleotide with the nucleic acid template and wherein the inactive oligonucleotide is activated by a nucleic acid metabolizing enzyme, wherein the nucleic acid metabolizing enzyme is selected from the group consisting of a topoisomerase, a helicase, a telomerase and a reverse transcriptase.

2. The process of claim 1, wherein the inactive oligonucleotide has a 3′

end block.

3. The process of claim 1, wherein the nucleic acid metabolizing enzyme is a topoisomerase.

4. The process of claim 1, wherein the nucleic acid metabolizing enzyme is a helicase.

5. The process of claim 1, wherein the nucleic acid metabolizing enzyme is a telomerase.

6. The process of claim 1, wherein the nucleic acid metabolizing enzyme is a reverse transcriptase.

7. The process of claim 1, wherein the extension is performed in the presence of four nucleoside triphosphates and a nucleic acid polymerase.

8. The process of claim 1, wherein the oligonucleotide is at least partially hybridized to the template before and during the first reaction.

9. The process of claim 1, wherein the extension is part of an amplification of the nucleic acid template.