Cleaved amplified modified polymorphic sequence detection methods
First Claim
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1. A method for detecting the presence or absence of a single nucleotide polymorphism in a nucleic acid molecule, said method comprising the steps of:
- (a) providing a nucleic acid molecule comprising a first strand, a second strand, and a nucleotide position suspected of comprising a polymorphism;
(b) amplifying a portion of said nucleic acid molecule by PCR using a first primer and a second primer, wherein (i) said first primer comprises a 3'"'"' region that is complementary to a first region of said first strand, the 5'"'"' end of said first region being positioned within 15 nucleotides 3'"'"' of said nucleotide position, and said 3'"'"' region of said first primer comprising at least one nucleotide mismatch with said first region within 15 nucleotides of said nucleotide position, (ii) said second primer comprises a 3'"'"' region that is complementary to a second region of said second strand, the 5'"'"' end of said second region being positioned 3'"'"' of said nucleotide position, and (iii) said amplification generates a PCR product comprising at least one point mutation, relative to the sequence of said nucleic acid molecule, that forms a portion of a restriction endonuclease recognition site in the presence of a single polymorphic nucleotide in said nucleotide position;
(c) labeling one end of one strand of the product of step (b) with a detectable label to generate a labeled PCR product comprising a labeled strand;
(d) treating said labeled PCR product with a restriction endonuclease that recognizes said restriction endonuclease recognition site to generate a digestion product;
(e) denaturing and contacting said digestion product with a probe that (i) is complementary to a first segment of said labeled strand that is on the opposite side of said nucleotide position from said detectable label, within said labeled strand, (ii) is not complementary to said labeled strand between said nucleotide position and said detectable label, and (iii) is immobilized to a binding element on a solid support; and
(f) assaying for said detectable label bound to said binding element, wherein the absence of said label bound to said binding element indicates the presence of said single nucleotide polymorphism in said nucleic acid molecule, and the presence of said label bound to said binding element indicates the absence of said single nucleotide polymorphism in said nucleic acid molecule.
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Abstract
The invention features methods for detecting polymorphic restriction sites and single nucleotide polymorphisms in nucleic acid molecules and kits for carrying out these methods.
82 Citations
35 Claims
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1. A method for detecting the presence or absence of a single nucleotide polymorphism in a nucleic acid molecule, said method comprising the steps of:
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(a) providing a nucleic acid molecule comprising a first strand, a second strand, and a nucleotide position suspected of comprising a polymorphism; (b) amplifying a portion of said nucleic acid molecule by PCR using a first primer and a second primer, wherein (i) said first primer comprises a 3'"'"' region that is complementary to a first region of said first strand, the 5'"'"' end of said first region being positioned within 15 nucleotides 3'"'"' of said nucleotide position, and said 3'"'"' region of said first primer comprising at least one nucleotide mismatch with said first region within 15 nucleotides of said nucleotide position, (ii) said second primer comprises a 3'"'"' region that is complementary to a second region of said second strand, the 5'"'"' end of said second region being positioned 3'"'"' of said nucleotide position, and (iii) said amplification generates a PCR product comprising at least one point mutation, relative to the sequence of said nucleic acid molecule, that forms a portion of a restriction endonuclease recognition site in the presence of a single polymorphic nucleotide in said nucleotide position; (c) labeling one end of one strand of the product of step (b) with a detectable label to generate a labeled PCR product comprising a labeled strand; (d) treating said labeled PCR product with a restriction endonuclease that recognizes said restriction endonuclease recognition site to generate a digestion product; (e) denaturing and contacting said digestion product with a probe that (i) is complementary to a first segment of said labeled strand that is on the opposite side of said nucleotide position from said detectable label, within said labeled strand, (ii) is not complementary to said labeled strand between said nucleotide position and said detectable label, and (iii) is immobilized to a binding element on a solid support; and (f) assaying for said detectable label bound to said binding element, wherein the absence of said label bound to said binding element indicates the presence of said single nucleotide polymorphism in said nucleic acid molecule, and the presence of said label bound to said binding element indicates the absence of said single nucleotide polymorphism in said nucleic acid molecule. - 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)
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28. A method for detecting the presence of a first single nucleotide polymorphism or a second single nucleotide polymorphism at a nucleotide position in a nucleic acid molecule, said method comprising the steps of:
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(a) providing a first aliquot of a nucleic acid molecule, said nucleic acid molecule comprising a first strand, a second strand, and a nucleotide position suspected of comprising a polymorphism; (b) amplifying a portion of said nucleic acid molecule by PCR using a first primer and a second primer, wherein (i) said first primer comprises a 3'"'"' region that is complementary to a first region of said first strand, the 5'"'"' end of said first region being positioned within 15 nucleotides 3'"'"' of said nucleotide position, and said 3'"'"' region of said first primer comprising at least one nucleotide mismatch with said first region within 15 nucleotides of said nucleotide position, (ii) said second primer comprises a 3'"'"' region that is complementary to a second region of said second strand, the 5'"'"' end of said second region being positioned 3'"'"' of said nucleotide position, and (iii) said amplification generates a first PCR product comprising at least one point mutation, relative to the sequence of said nucleic acid molecule, that forms a portion of a first restriction endonuclease recognition site in the presence of a first single polymorphic nucleotide in said nucleotide position; (c) labeling one end of one strand of the product of step (b) with a detectable label to generate a first labeled PCR product comprising a labeled strand; (d) treating said first labeled PCR product with a first restriction endonuclease that recognizes said first restriction endonuclease recognition site to generate a first digestion product; (e) denaturing and contacting said first digestion product with a first probe that (i) is complementary to a first segment of said labeled strand that is on the opposite side of said nucleotide position from said detectable label, within said labeled strand, (ii) is not complementary to said labeled strand between said nucleotide position and said detectable label, and (iii) is immobilized on a first binding element; (f) assaying for said detectable label bound to said first binding element; (g) providing a second aliquot of said nucleic acid molecule; (h) amplifying a portion of said nucleic acid molecule by PCR using a third primer and a fourth primer, wherein (i) said third primer comprises a 3'"'"' region that is complementary to a first region of said first strand, the 5'"'"' end of said first region being positioned within 15 nucleotides 3'"'"' of said nucleotide position, and said 3'"'"' region of said third primer comprising at least one nucleotide mismatch with said first region within 15 nucleotides of said nucleotide position, (ii) said fourth primer comprises a 3'"'"' region that is complementary to a second region of said second strand, the 5'"'"' end of said second region being positioned 3'"'"' of said nucleotide position, and (iii) said amplification generates a second PCR product comprising at least one point mutation, relative to the sequence of said nucleic acid molecule, that forms a portion of a second restriction endonuclease recognition site in the presence of a second single polymorphic nucleotide in said nucleotide position; (i) labeling one end of one strand of the product of step (h) with a detectable label to generate a second labeled PCR product comprising a labeled strand; (j) treating said second labeled PCR product with a second restriction endonuclease that recognizes said second restriction endonuclease recognition site to generate a second digestion product; (k) denaturing and contacting said second digestion product with a second probe that (i) is complementary to a first segment of said labeled strand that is on the opposite side of said nucleotide position from said detectable label, within said labeled strand, (ii) is not complementary to said labeled strand between said nucleotide position and said detectable label, and (iii) is immobilized on a second binding element; and (l) assaying for said detectable label bound to said second binding element, wherein (i) the absence of said label bound to said first binding element indicates the presence of said first single nucleotide polymorphism;
(ii) the absence of said label bound to said second binding element indicates the presence of said second single nucleotide polymorphism; and
(iii) the absence of said label bound to both of said first binding element and said second binding element indicates the presence of said first single nucleotide polymorphism and said second single nucleotide polymorphism.
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29. A kit for detecting the presence or absence of a single nucleotide polymorphism in a nucleic acid molecule comprising:
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(a) a first primer and a second primer flanking a nucleotide position suspected of comprising a polymorphism, wherein (i) said first primer comprises a 3'"'"' region that is complementary to a first region of a first strand of said nucleic acid molecule, the 5'"'"' end of said first region being positioned within 15 nucleotides 3'"'"' of said nucleotide position, and said 3'"'"' region of said first primer comprising at least one nucleotide mismatch with said first region within 15 nucleotides of said nucleotide position, and (ii) said second primer comprises a 3'"'"' region that is complementary to a second region of a second strand of said nucleic acid molecule, the 5'"'"' end of said second region being positioned 3'"'"' of said nucleotide position, wherein amplifying said nucleic acid molecule using said first primer and said second primer generates a PCR product comprising at least one point mutation, relative to the sequence of said nucleic acid molecule, that forms a portion of a restriction endonuclease recognition site in the presence of a single polymorphic nucleotide in said nucleotide position; and (b) a probe that either (i) is complementary to a first segment of said second strand and that is on the opposite side of said nucleotide position from said first primer and is not complementary to said second strand between said nucleotide position and said first primer, or (ii) is complementary to a first segment of said first strand that is on the opposite side of said nucleotide position from said second primer and is not complementary to said first strand between said nucleotide position and said second primer, said probe being immobilized to a binding element on a solid support. - View Dependent Claims (30, 31, 32, 33, 34, 35)
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Specification