Polymorphism detection and separation
First Claim
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1. A method of distinguishing the presence of a nonsupercoiled target nucleic acid from the presence of nonsupercoiled target variants within a sample of nucleic acids having a common target query region, the method comprising:
- providing a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotides is bound by a recombinase and said second oligonucleotide is free of a recombinase;
adding said first oligonucleotide to the sample to form a mixture;
adding said second oligonucleotide to the mixture to form a double D loop;
deproteinizing the double D loop; and
distinguishing the double D loops that are stable to deproteinization, wherein the presence of a stable double D loop distinguishes the presence of target from that of variants;
wherein the first oligonucleotide comprises a complementarity region that is perfectly complementary to a first strand of the target across the entirety of the target query region and wherein the second oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a second strand of the target across at least a portion of the target query region, and at least one of said first or second oligonucleotide complementarity regions is imperfectly complementary to at least one of a first strand or a second strand of the query region of the target variants.
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Abstract
Methods and compositions for polymorphism detection and separation. The methods are readily multiplexed, can be adapted to a variety of existing detection systems, and permit target amplification without PCR. The methods permit allelic variants selectively to be isolated, with or without contemporaneous detection, and finds particular utility in facilitating the construction of coisogenic cell collections in which the cells differ genotypically by single nucleotide changes targeted to defined loci.
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Citations
69 Claims
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1. A method of distinguishing the presence of a nonsupercoiled target nucleic acid from the presence of nonsupercoiled target variants within a sample of nucleic acids having a common target query region, the method comprising:
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providing a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotides is bound by a recombinase and said second oligonucleotide is free of a recombinase; adding said first oligonucleotide to the sample to form a mixture; adding said second oligonucleotide to the mixture to form a double D loop; deproteinizing the double D loop; and distinguishing the double D loops that are stable to deproteinization, wherein the presence of a stable double D loop distinguishes the presence of target from that of variants; wherein the first oligonucleotide comprises a complementarity region that is perfectly complementary to a first strand of the target across the entirety of the target query region and wherein the second oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a second strand of the target across at least a portion of the target query region, and at least one of said first or second oligonucleotide complementarity regions is imperfectly complementary to at least one of a first strand or a second strand of the query region of the target variants. - 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53)
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54. A method of distinguishably detecting the presence of a plurality of nonsupercoiled targets within a sample of nucleic acids, the method comprising:
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for each of the plurality of targets desired to be detected, providing a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotide is bound by a recombinase and said second oligonucleotide is free of a recombinase; wherein said first oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a first strand of its respective target across the entirety of the target query region, and said second oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a second strand of the same target across at least a portion of the target query region and at least one of said oligonucleotide regions is imperfectly complementary in sequence to respective first and second strands of the query region of each of the other targets desired discriminably to be detected; adding said first oligonucleotide to the sample to form a mixture; adding said second oligonucleotide to the mixture to form a double D loop; deproteinizing the double D loop to form at least one deproteinization-stable double D loop; and distinguishably detecting at least one deproteinization-stable double D loop formed in the target query region, each target double D loop being distinguishably detectable from all others of the double D loops formed in said sample. - View Dependent Claims (55, 56, 57, 58, 59, 60, 61)
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62. A method of separating a nonsupercoiled double stranded nucleic acid target from other nonsupercoiled nucleic acids present within a sample of nucleic acids, the method comprising:
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providing a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotide is bound by a recombinase and said second oligonucleotides is free of a recombinase; wherein said first oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a first strand of the target across the entirety of the target query region, and said second oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a second strand of the target across at least a portion of the target query region, and at least one of said first or second oligonucleotide complementarity regions is imperfectly complementary to the respective first and second strands of the query region of each of said other nonsupercoiled nucleic acids; adding said first oligonucleotide to the sample to form a mixture; adding said second oligonucleotide to the mixture to form a double D loop; deproteinizing the double D loop to form at least one deproteinization-stable double D loop; and separating nucleic acids having at least one deproteinization-stable double D loop in the query region of the target, from other nucleic acids present within said sample. - View Dependent Claims (63, 64, 65, 66)
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67. A method of distinguishing the presence of a supercoiled target nucleic acid from the presence of supercoiled target variants within a sample of nucleic acids, the variants differing from the target by as few as one nucleotide within a common target query region, the method comprising:
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providing a first oligonucleotide and a second oligonucleotide, wherein said first oligonucleotide is bound by a recombinase and wherein said second oligonucleotide is free of a recombinase; wherein the first oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a first strand of the target across the entirety of the target query region, said region being imperfectly complementary to a first strand of the query region of each of said target variants, wherein the first oligonucleotide mediates formation of at least one deproteinization-stable double D loop in the query region of the target; wherein said second oligonucleotide includes a complementarity region that is perfectly complementary in sequence to a second strand of the target across at least a portion of the target query region; adding said first oligonucleotide to the sample to form a mixture; adding said second oligonucleotide to the mixture to form a double D loop; deproteinizing the double D loop; and distinguishing the double D loops that are stable to deproteinization, wherein the presence of a stable double D loop distinguishes the presence of target from that of variants.
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- 68. The method of 67, wherein at least one of said first and second oligonucleotide complementarity regions is imperfectly complementary to respective strand of the query region of each of said target variants, and wherein said second oligonucleotide comprises base modifications and wherein said second oligonucleotide is distinguishably detectable.
Specification