Methods and compositions for universal size-specific PCR
First Claim
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1. A method of enriching for a target nucleic acid in a sample containing a mixture of target and non-target nucleic acid, comprising the steps of:
- a) introducing to the sample a pair of forward and reverse inside primers that bind target and non-target nucleic acid, wherein;
(i) the target nucleic acid is a low copy number, relatively short nucleic acid of at least about 75 base pairs, but less than about 1200 base pairs and the non-target nucleic acid is an abundant copy number nucleic acid that is longer than the target nucleic acid, and(ii) the inside primers comprise a common, universal domain and a sequence-specific domain complementary to both the target and non-target nucleic acids;
b) introducing to the sample an outside non-target binding primer at a concentration two times or more greater than the inside primer, wherein;
(i) the inside primers and outside primer are introduced to the sample at a concentration greater than the concentration of non-target nucleic acid, and(ii) the outside non-target binding primer anneals upstream or downstream of the inside primer and is complementary to non-target nucleic acid, but not target nucleic acid;
c) introducing to the sample a universal primer capable of binding to the universal domain of the inside primers, wherein the universal primer is introduced at a concentration greater than the outside primer;
d) performing an amplification reaction using a polymerase having exonuclease activity, wherein;
(i) amplification of the non-target nucleic acid is initiated by the outside primer bound to one strand of the non-target nucleic acid, whereby the exonuclease activity digests the inside primer bound to the same strand of the non-target nucleic acid;
(ii) the outside primer does not bind to the target nucleic acid and amplification of the target nucleic acid is not initiated by the outside primer; and
(iii) amplification of the target nucleic acid is initiated by the inside primers, whereby the target nucleic acid is preferentially amplified relative to the non-target nucleic acid and whereby the target nucleic acid in the sample is enriched.
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Abstract
Provided herein are products and processes for the amplification, detection and sequencing of short-stranded nucleic acid in the presence of a high background of long-stranded genomic material (e.g., host or maternal nucleic acids). The methods rely on the use of inside and outside primers introduced at varying concentrations, as well as universal amplification reactions that preferentially amplify short, low copy number nucleic acid.
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34 Claims
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1. A method of enriching for a target nucleic acid in a sample containing a mixture of target and non-target nucleic acid, comprising the steps of:
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a) introducing to the sample a pair of forward and reverse inside primers that bind target and non-target nucleic acid, wherein; (i) the target nucleic acid is a low copy number, relatively short nucleic acid of at least about 75 base pairs, but less than about 1200 base pairs and the non-target nucleic acid is an abundant copy number nucleic acid that is longer than the target nucleic acid, and (ii) the inside primers comprise a common, universal domain and a sequence-specific domain complementary to both the target and non-target nucleic acids; b) introducing to the sample an outside non-target binding primer at a concentration two times or more greater than the inside primer, wherein; (i) the inside primers and outside primer are introduced to the sample at a concentration greater than the concentration of non-target nucleic acid, and (ii) the outside non-target binding primer anneals upstream or downstream of the inside primer and is complementary to non-target nucleic acid, but not target nucleic acid; c) introducing to the sample a universal primer capable of binding to the universal domain of the inside primers, wherein the universal primer is introduced at a concentration greater than the outside primer; d) performing an amplification reaction using a polymerase having exonuclease activity, wherein; (i) amplification of the non-target nucleic acid is initiated by the outside primer bound to one strand of the non-target nucleic acid, whereby the exonuclease activity digests the inside primer bound to the same strand of the non-target nucleic acid; (ii) the outside primer does not bind to the target nucleic acid and amplification of the target nucleic acid is not initiated by the outside primer; and (iii) amplification of the target nucleic acid is initiated by the inside primers, whereby the target nucleic acid is preferentially amplified relative to the non-target nucleic acid and whereby the target nucleic acid in the sample is enriched. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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Specification