Pyrophosphorolysis activated polymerization (PAP)
First Claim
1. A method for determining the presence or absence of a nucleic acid hybrid in a sample comprising the following steps:
- (a) providing a reaction mixture comprising (i) a sample that may contain a nucleic acid hybrid wherein one strand of the hybrid comprises an activatable oligonucleotide having a non-extendible 3′
-terminus, (ii) pyrophosphate, (iii) an enzyme that catalyzes the release of a nucleotide from a nucleic acid hybrid, by pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of the nucleic acid hybrid in the presence of pyrophosphate, and (iv) a suitable nucleotide that can be incorporated in the place of said released nucleotide;
(b) maintaining said reaction mixture for a time period and under conditions that permit (i) pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of a nucleic acid hybrid to produce a released nucleotide and a modified 3′
-terminus as well as (ii) the incorporation of said suitable nucleotide into the modified 3′
-terminus of the nucleic acid hybrid to produce an incorporated modified 3′
-terminus, thereby forming a treated sample; and
(c) assaying the treated sample to determine whether incorporation of said suitable nucleotide into the hybrid occurred and thereby determining the presence or absence of a nucleic acid hybrid in said sample.
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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.
21 Citations
23 Claims
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1. A method for determining the presence or absence of a nucleic acid hybrid in a sample comprising the following steps:
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(a) providing a reaction mixture comprising (i) a sample that may contain a nucleic acid hybrid wherein one strand of the hybrid comprises an activatable oligonucleotide having a non-extendible 3′
-terminus, (ii) pyrophosphate, (iii) an enzyme that catalyzes the release of a nucleotide from a nucleic acid hybrid, by pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of the nucleic acid hybrid in the presence of pyrophosphate, and (iv) a suitable nucleotide that can be incorporated in the place of said released nucleotide;(b) maintaining said reaction mixture for a time period and under conditions that permit (i) pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of a nucleic acid hybrid to produce a released nucleotide and a modified 3′
-terminus as well as (ii) the incorporation of said suitable nucleotide into the modified 3′
-terminus of the nucleic acid hybrid to produce an incorporated modified 3′
-terminus, thereby forming a treated sample; and(c) assaying the treated sample to determine whether incorporation of said suitable nucleotide into the hybrid occurred and thereby determining the presence or absence of a nucleic acid hybrid in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 20, 21)
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9. A method for determining the presence or absence of a nucleic acid target in a sample comprising the following steps:
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(a) providing a reaction mixture comprising (i) a sample that may contain a nucleic acid target, (ii) a nucleic acid probe corresponding to said nucleic acid target, wherein the nucleic acid probe comprises an activatable oligonucleotide having a non-extendible 3′
terminus, (iii) pyrophosphate, (iv) an enzyme that catalyzes the release of a nucleotide from a nucleic acid hybrid, wherein one strand of the hybrid comprises an activatable oligonucleotide having a non-extendible 3′
-terminus, by pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of the nucleic acid hybrid in the presence of pyrophosphate, and (v) a suitable nucleotide that can be incorporated in the place of said released nucleotide;(b) maintaining said reaction mixture for a time period and under conditions that permit (i) hybridization of the nucleic acid target with the nucleic acid probe to form a nucleic acid hybrid that comprises a non-extendible 3′
-terminus, (ii) pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of a nucleic acid hybrid to produce a released nucleotide and a modified 3′
-terminus as well as (iii) the incorporation of said suitable nucleotide into the modified 3′
-terminus of the nucleic acid hybrid to produce an incorporated modified 3′
-terminus, thereby forming a treated sample; and(c) assaying the treated sample to determine whether incorporation of said suitable nucleotide occurred and thereby determining the presence or absence of the nucleic acid target in said sample. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16)
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17. A method for determining the presence or absence of a specific nucleic acid base at an interrogation position of a nucleic acid target in a sample comprising the following steps:
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(a) providing a reaction mixture comprising (i) a sample that may contain a nucleic acid target having a nucleic acid residue at an interrogation position, (ii) a nucleic acid probe comprising a nucleic acid residue in its 3′
-terminus that base pairs with the interrogation position of the nucleic acid target when the nucleic acid target and the nucleic acid probe are hybridized to form a nucleic acid hybrid, wherein the nucleic acid probe comprises an activatable oligonucleotide having a non-extendible 3′
terminus, (ii) pyrophosphate, (iii) an enzyme that catalyzes the release of a nucleotide from a nucleic acid hybrid, a wherein one strand of the hybrid comprises an activatable oligonucleotide having a non-extendible 3′
-terminus, by pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of the nucleic acid hybrid in the presence of pyrophosphate, and (iv) a suitable nucleotide that can be incorporated in the place of said released nucleotide;(b) maintaining said reaction mixture for a time period and under conditions that permit (i) formation of a nucleic acid hybrid between the nucleic acid probe and the nucleic acid target, (ii) pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of a nucleic acid hybrid to produce a released nucleotide and a modified 3′
-terminus and (iii) the incorporation of said suitable nucleotide into the modified 3′
-terminus of the nucleic acid hybrid to produce an incorporated modified 3′
-terminus, thereby forming a treated sample; and(c) assaying the treated sample to determine whether incorporation of said suitable nucleotide occurred and thereby determining the presence or absence of a specific nucleic acid base at an interrogation position of a nucleic acid target in said sample. - View Dependent Claims (18, 19)
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22. A method of determining a nucleotide sequence of a nucleic acid hybrid that comprises the following steps:
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(a) providing a reaction mixture comprising (i) a sample that contains a nucleic acid hybrid wherein one strand of the hybrid comprises an activatable oligonucleotide having a non-extendible 3′
-terminus, (ii) pyrophosphate, (iii) an enzyme that catalyzes the release of a nucleotide from a nucleic acid hybrid, by pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of the nucleic acid hybrid in the presence of pyrophosphate, and (iv) a suitable nucleotide that can be incorporated in the place of said released nucleotide;(b) maintaining said reaction mixture for a time period and under conditions that permit (i) pyrophosphorolysis of the non-extendible 3′
-terminus of a strand of a nucleic acid hybrid to produce a released nucleotide and a modified 3′
-terminus as well as (ii) the incorporation of said suitable nucleotide into the modified 3′
-terminus of the nucleic acid hybrid to produce an incorporated modified 3′
-terminus, thereby forming a treated sample; and(c) assaying the treated sample to determine where incorporation of said suitable nucleotide into the hybrid occurred and thereby determining nucleotide sequence of the nucleic acid hybrid. - View Dependent Claims (23)
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Specification