Cleaved amplified RFLP detection methods
First Claim
Patent Images
1. A method for identifying a polymorphic restriction site in a nucleic acid, said method comprising the steps of:
- (a) digesting DNA isolated from a first sample of an organism with a first restriction endonuclease to generate a first reaction product;
(b) ligating to each of the ends of said first reaction product a first adaptor to generate a second reaction product;
(c) digesting said second reaction product with a second restriction endonuclease to generate a third reaction product;
(d) ligating to each of the ends of said third reaction product a second adaptor to generate a fourth reaction product;
(e) amplifying said fourth reaction product to generate a fifth reaction product by PCR using a first primer complementary to said first adaptor and a second primer complementary to said second adaptor, said second primer being tagged with a first member of a specific binding pair;
(f) in a separate set of reactions, digesting DNA isolated from a second sample from said organism with said first restriction endonuclease to generate a sixth reaction product;
(g) ligating to each of the ends of said sixth reaction product a third adaptor to generate a seventh reaction product;
(h) digesting said seventh reaction product with said second restriction endonuclease to generate an eighth reaction product;
(i) denaturing said fifth reaction product to generate a ninth reaction product and denaturing said eighth reaction product to generate a tenth reaction product;
(j) combining said ninth and tenth reaction products under conditions allowing hybridization to generate an eleventh reaction product;
(k) contacting said eleventh reaction product with the second member of said specific binding pair, said second member being immobilized on a solid support;
(l) recovering any of said eleventh reaction product captured on said solid support to generate a twelfth reaction product; and
(m) amplifying said twelfth reaction product by PCR using a primer complementary to said third adaptor, an amplified product being an indication of a polymorphic restriction site that is recognized by said second restriction endonuclease.
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Abstract
The invention features methods for detecting polymorphic restriction sites in nucleic acids and kits for carrying out these methods.
53 Citations
66 Claims
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1. A method for identifying a polymorphic restriction site in a nucleic acid, said method comprising the steps of:
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(a) digesting DNA isolated from a first sample of an organism with a first restriction endonuclease to generate a first reaction product; (b) ligating to each of the ends of said first reaction product a first adaptor to generate a second reaction product; (c) digesting said second reaction product with a second restriction endonuclease to generate a third reaction product; (d) ligating to each of the ends of said third reaction product a second adaptor to generate a fourth reaction product; (e) amplifying said fourth reaction product to generate a fifth reaction product by PCR using a first primer complementary to said first adaptor and a second primer complementary to said second adaptor, said second primer being tagged with a first member of a specific binding pair; (f) in a separate set of reactions, digesting DNA isolated from a second sample from said organism with said first restriction endonuclease to generate a sixth reaction product; (g) ligating to each of the ends of said sixth reaction product a third adaptor to generate a seventh reaction product; (h) digesting said seventh reaction product with said second restriction endonuclease to generate an eighth reaction product; (i) denaturing said fifth reaction product to generate a ninth reaction product and denaturing said eighth reaction product to generate a tenth reaction product; (j) combining said ninth and tenth reaction products under conditions allowing hybridization to generate an eleventh reaction product; (k) contacting said eleventh reaction product with the second member of said specific binding pair, said second member being immobilized on a solid support; (l) recovering any of said eleventh reaction product captured on said solid support to generate a twelfth reaction product; and (m) amplifying said twelfth reaction product by PCR using a primer complementary to said third adaptor, an amplified product being an indication of a polymorphic restriction site that is recognized by said second restriction endonuclease. - View Dependent Claims (2, 51, 52, 53, 60)
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3. A kit for identifying a polymoiphic restriction site in a nucleic acid, said kit comprising:
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(a) a first DNA adaptor, a second DNA adaptor, and a third DNA adaptor, said first and third DNA adaptors comprising regions complementary to the ends generated by a first restriction endonuclease ends but differing in overall sequence and said second DNA adaptor comprising a region complementary to the ends generated by a second restriction endonuclease, said second restriction endonuclease site corresponding to said polymorphic restriction site; and (b) a first primer, a second primer, and a third primer, said first primer hybridizing to said first DNA adaptor, said second primer hybridizing to said second DNA adaptor and being tagged with a first member of a specific binding pair, and said third primer hybridizing to said third DNA adaptor. - View Dependent Claims (4)
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5. A method for detecting the presence or absence of a polymorphic restriction site in a nucleic acid, said method comprising the steps of:
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(a) amplifying said nucleic acid by PCR using a first and a second primer flanking said polymorphic restriction site, said first primer being tagged with a detectable label, wherein said amplifying generates a PCR product comprising a first strand tagged with said detectable label and an unlabeled second strand; (b) treating said PCR product with a restriction endonuclease that recognizes said polymorphic restriction site to generate a digestion product; (c) denaturing said digestion product to generate a denatured product; (d) contacting said denatured product with a first probe, said first probe comprising a sequence that hybridizes to a first sequence in said first strand, said first sequence being between said polymorphic restriction site and the sequence in said first strand that is complementary to said second primer, said first probe being immobilized on a first binding element; (e) monitoring said first binding element for the presence of said detectable label, wherein detection of said detectable label on said first binding element indicates the absence of said polymorphic restriction site in said nucleic acid, and a failure to detect said detectable label on said first binding element indicates the presence of said polymorphic restriction site in said nucleic acid. - View Dependent Claims (6, 7, 8, 9, 10, 11, 12, 54, 55, 56, 61)
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13. A method for detecting the presence or absence of a polymorphic restriction site in a nucleic acid, said method comprising the steps of:
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(a) amplifying said nucleic acid by PCR using a first and a second primer flanking said polymorphic restriction site, said first primer being tagged with a first detectable label, said second primer being tagged with a second detectable label, wherein said amplifying generates a PCR product comprising a first strand tagged with said first detectable label and a second strand tagged with said second detectable label; (b) treating said PCR product with a restriction endonuclease that recognizes said polymorphic restriction site to generate a digestion product; (c) denaturing said digestion product to generate a denatured product; (d) contacting said denatured product with a first and a second probe, said first probe comprising a sequence that hybridizes to a first sequence in said first strand, said first sequence being between said polymorphic restriction site and the sequence in said first strand that is complementary to said second primer, said first probe being immobilized on a first binding element;
said second probe comprising a sequence that hybridizes to a second sequence in said second strand, said second sequence being between said polymorphic restriction site and the sequence in said second strand that is complementary to said first primer, said second probe being immobilized on a second binding element;(e) monitoring said first binding element for the presence of said first detectable label and monitoring said second binding element for the presence of said second detectable label, wherein detection of said first detectable label on said first binding element and detection of said second detectable label on said second binding element indicates the absence of said polymorphic restriction site in said nucleic acid, and a failure to detect said first detectable label on said first binding element and a failure to detect said second detectable label on said second binding element indicates the presence of said polymorphic restriction site in said nucleic acid. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 57, 58, 59, 62)
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22. A method for determining whether an organism is homozygous for a polymorphic restriction site, is heterozygous for said polymorphic restriction site, or lacks said polymorphic restriction site, said method comprising the steps of:
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(a) carrying out PCR on a sample comprising nucleic acid molecules from the organism using a first and a second primer flanking said polymorphic restriction site, wherein said amplifying generates a PCR product comprising a first strand comprising a sequence that is identical to the sequence of said first primer and a second strand comprising a sequence that is identical to the sequence of said second primer; (b) treating said PCR product with a restriction endonuclease that recognizes said polymorphic restriction site to generate a digestion product; (c) denaturing said digestion product to generate a denatured product; (d) contacting said denatured product with an oligonucleotide to generate a first reaction product, said oligonucleotide comprising a 3'"'"' portion that hybridizes to a first region in said first strand, said first region being between said polymorphic restriction site and a sequence in said first strand that is identical to the sequence of said first primer, said oligonucleotide being blocked so that it cannot serve as a primer for DNA polymerase, said oligonuclcotidc comprising a 5'"'"' portion that does not hybridize to said first strand; (e) treating said first reaction product with a DNA polymerase to extend any unblocked, primed 3'"'"' end in said first reaction product to generate a second reaction product; (f) amplifying said second reaction product by PCR using a third primer, said third primer having a sequence identical to said first primer and being tagged with a first detectable label, and a fourth primer that hybridizes to a sequence that is complementary to said 5'"'"' portion of said oligonucleotide to generate a second PCR product, said fourth primer being tagged with a second detectable label; (g) denaturing said second PCR product to generate a second denatured product; (h) contacting said second denatured product with a first and a second probe, said first probe comprising a sequence that hybridizes to a first sequence in said second strand, said first sequence being between said polymorphic restriction site and the sequence in said second strand that is complementary to said first primer, said first probe being immobilized on a first binding element;
said second probe comprising a sequence that hybridizes to a second sequence in said first strand, said second sequence being between said polymorphic restriction site and the sequence in said first strand that is complementary to said second primer, said second probe being immobilized on a second binding clement;(i) monitoring said first binding element for the presence of said second detectable label and monitoring said second binding element for the presence of said first detectable label, wherein detection of said second detectable label on said first binding element and detection of said first detectable label on said second binding element indicates that the organism is heterozygous for said polymorphic restriction site, detection of said second detectable label on said first binding element and a failure to detect said first detectable label on said second binding element indicates that the organism is a homozygote comprising said polymorphic restriction site, and detection of said first detectable label on said second binding element and a failure to detect said second detectable label on said first binding element indicates that the organism is a homozygote lacking said polymorphic restriction site. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29, 30, 63, 64, 65, 66)
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31. A kit for detecting the presence or absence of a polymorphic restriction site in a nucleic acid, said kit comprising:
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a first and a second primer flanking said polymorphic restriction site, said first primer being tagged with a detectable label, wherein amplifying said nucleic acid by PCR with said first and second primers generates a PCR product comprising a first strand tagged with said detectable label and a second strand; and a first probe that comprises a sequence that hybridizes to a first sequence in said first strand, said first sequence being between said polymorphic restriction site and the sequence in said first strand that is complementary to said second primer, and said first probe is immobilized on a first binding element. - View Dependent Claims (32, 33, 34, 35, 36, 37, 38, 39, 40, 41)
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42. A kit for detecting the presence or absence of a polymorphic restriction site in a nucleic acid, said kit comprising:
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a first and a second PCR primer flanking said polymorphic restriction site, said first primer being tagged with a first detectable label, wherein amplifying said nucleic acid by PCR using said first and second primers generates a PCR product comprising a first strand tagged with said first detectable label and a second strand; an oligonucleotide comprising a 3'"'"' portion that hybridizes to a first region in said first strand, said first region flanking said polymorphic restriction site on the side of said polymorphic restriction site comprising a sequence that is identical to the sequence of said first primer, said oligonucleotide being blocked so that it cannot serve as a primer for DNA polymerase, said oligonucleotide comprising a 5'"'"' portion that does not hybridize to a second region in said first strand, said second region flanking said polymorphic restriction site on the side of said polymorphic restriction site comprising a sequence that is complementary to said second primer; a third primer that hybridizes to a sequence that is complementary to said 5'"'"' portion of said oligonucleotide, said third primer being tagged with a second detectable label; a first and a second probe, said first probe comprising a sequence that hybridizes to a first sequence in said second strand, said first sequence being between said polymorphic restriction site and the sequence in said second strand that is complementary to said first primer, said first probe being immobilized on a first binding element;
said second probe comprising a sequence that hybridizes to a second sequence in said first strand, said second sequence being between said polymorphic restriction site and the sequence in said first strand that is complementary to said second primer, and said second probe being immobilized on a second binding element. - View Dependent Claims (43, 44, 45, 46, 47, 48, 49, 50)
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Specification