Repair-mediated process for amplifying and detecting nucleic acid sequences
First Claim
1. A process for detecting a specific nucleic acid target molecule in a sample by amplifying the nucleic acid target molecule, the process comprising the steps of:
- a) treating the sample with at least two oligonucleotides for each strand of the target molecule, under hybridizing conditions,i) wherein the oligonucleotides are selected so as to be sufficiently complementary to each strand of the target molecule to hybridize therewith under the hybridizing conditions; and
ii) wherein a gap of one or more bases is present between two oligonucleotides when the two oligonucleotides are hybridized to a strand of the target molecule; and
iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps;
b) filling the gaps formed in step (a) with one or more bases complementary to the base or bases in the gaps and joining the base or bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming a joined oligonucleotide product;
c) treating the hybridized joined oligonucleotide product of step (b) under denaturing conditions to separate the joined oligonucleotide products from the target molecule to produce single-stranded molecules;
d) treating the single-stranded molecules produced in step (c) with an excess of at least two oligonucleotide complement pairs, under hybridizing conditions,i) wherein each oligonucleotide complement pair comprises two oligonucleotides selected so as to be sufficiently complementary to each other, to each strand of the target molecule and to the joined oligonucleotide products to hybridize therewith under the hybridizing conditions; and
ii) wherein gaps of one or more bases are present between the oligonucleotides when the oligonucleotides are hybridized to each strand of the target molecule; and
iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps;
e) filling in the gaps formed in step (d) with one or more bases complementary to the base or bases in the gaps and joining the bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming additional joined oligonucleotide products, resulting in the amplification of the target molecule; and
f) detecting the joined oligonucleotide products.
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Abstract
This invention relates to a process for amplifying and detecting any desired specific nucleic acid sequence that exists in a nucleic acid or mixture thereof. The process comprises treating single strand RNA or separated complementary strands of DNA target with a molar excess of oligonucleotide complement pairs in which these oligonucleotide complement pairs have sequences complementary to the target, under hybridizing conditions. In one embodiment, the oligonucleotide complement pairs may have a gap of one or more bases which may be repaired (filled) by enzymes. The oligonucleotide complement pairs are joined together, forming joined, oligonucleotide product. The target/joined product hybrid nucleic acids are then denatured to single strands again, at which point both the target and the joined products can form hybrids with new oligonucleotide complement pairs. The steps of the reaction may be carried out stepwise or simultaneously and can be repeated as often as desired.
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Citations
15 Claims
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1. A process for detecting a specific nucleic acid target molecule in a sample by amplifying the nucleic acid target molecule, the process comprising the steps of:
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a) treating the sample with at least two oligonucleotides for each strand of the target molecule, under hybridizing conditions, i) wherein the oligonucleotides are selected so as to be sufficiently complementary to each strand of the target molecule to hybridize therewith under the hybridizing conditions; and ii) wherein a gap of one or more bases is present between two oligonucleotides when the two oligonucleotides are hybridized to a strand of the target molecule; and iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps; b) filling the gaps formed in step (a) with one or more bases complementary to the base or bases in the gaps and joining the base or bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming a joined oligonucleotide product; c) treating the hybridized joined oligonucleotide product of step (b) under denaturing conditions to separate the joined oligonucleotide products from the target molecule to produce single-stranded molecules; d) treating the single-stranded molecules produced in step (c) with an excess of at least two oligonucleotide complement pairs, under hybridizing conditions, i) wherein each oligonucleotide complement pair comprises two oligonucleotides selected so as to be sufficiently complementary to each other, to each strand of the target molecule and to the joined oligonucleotide products to hybridize therewith under the hybridizing conditions; and ii) wherein gaps of one or more bases are present between the oligonucleotides when the oligonucleotides are hybridized to each strand of the target molecule; and iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps; e) filling in the gaps formed in step (d) with one or more bases complementary to the base or bases in the gaps and joining the bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming additional joined oligonucleotide products, resulting in the amplification of the target molecule; and f) detecting the joined oligonucleotide products. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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15. A process for detecting a specific nucleic acid target molecule in a sample by amplifying the nucleic acid target molecule, the process comprising the steps of:
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a) treating the sample with at least two oligonucleotides for each strand of the target molecule, under hybridizing conditions, i) wherein the oligonucleotides are selected so as to be sufficiently complementary to each strand of the target molecule to hybridize therewith under the hybridizing conditions; and ii) wherein a gap of more than one bases is present between two oligonucleotides when the two oligonucleotides are hybridized to a strand of the target molecule; and iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps; b) filling the gaps formed in step (a) with one or more bases complementary to the base or bases in the gaps and joining the base or bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming a joined oligonucleotide product; c) treating the hybridized joined oligonucleotide product of step (b) under denaturing conditions to separate the joined oligonucleotide products from the target molecule to produce single-stranded molecules; d) treating the single-stranded molecules produced in step (c) with an excess of at least two oligonucleotide complement pairs, under hybridizing conditions, i) wherein each oligonucleotide complement pair comprises two oligonucleotides selected so as to be sufficiently complementary to each other, to each strand of the target molecule and to the joined oligonucleotide products to hybridize therewith under the hybridizing conditions; and ii) wherein gaps of more than one bases are present between the oligonucleotides when the oligonucleotides are hybridized to each strand of the target molecule; and iii) wherein the oligonucleotides are selected so that the gaps between them will require less than all four types of bases to fill the gaps; e) filling in the gaps formed in step (d) with one or more bases complementary to the base or bases in the gaps and joining the bases filling the gaps to each other and to both adjacent hybridized oligonucleotides, thereby forming additional joined oligonucleotide products, resulting in the amplification of the target molecule; and f) detecting the joined oligonucleotide products.
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Specification