Methods and kits for methylation detection
First Claim
1. A method for determining the degree of methylation of a target nucleotide comprising, (a) reacting (1) a target sequence with (2) a first cleavage probe set comprising (i) a first cleavage probe comprising a sequence that is complementary to a first target region and (ii) a second cleavage probe comprising a sequence that is complementary to a second target region and that is downstream from a flap portion, wherein the second target region is located 5′
- of the first target region and overlaps the first target region by at least one nucleotide, under effective conditions for the first and second cleavage probes of the first cleavage probe set to anneal to the corresponding first and second target regions, respectively, forming a first hybridization complex;
(b) cleaving the flap portion of the second cleavage probe in the first hybridization complex to generate a cleaved flap and form a second hybridization complex comprising (1) the target sequence, (2) the first cleavage probe, and (3) an annealed fragment of the second cleavage probe having a 5′
-terminal nucleotide located adjacent to the 3′
-end of the annealed first cleavage probe;
(c) ligating the first cleavage probe to the annealed fragment of the second cleavage probe to generate a first ligation product and form a third hybridization complex comprising the target sequence and the first ligation product; and
(d) determining the degree of methylation of the target nucleotide.
3 Assignments
0 Petitions
Accused Products
Abstract
Methods for determining the methylation state of at least one target nucleotide that employ a reaction catalyzed by a structure-specific nuclease, typically coupled with a ligation reaction are disclosed. By detecting the cleaved flap, a ligation product, a ligation product surrogate, a hybridization complex, or combinations thereof, one can infer the degree to which the corresponding target nucleotide is methylated. Certain of the disclosed methods are particularly useful for evaluating bisulfite-treated target sequences and determining the degree of target nucleotide methylation. The disclosed methods are well suited for rapidly analyzing a large number of target sequences, typically in one or more multiplex reactions. Kits for performing coupled nuclease and ligase methylation detection assays are also disclosed.
34 Citations
20 Claims
-
1. A method for determining the degree of methylation of a target nucleotide comprising,
(a) reacting (1) a target sequence with (2) a first cleavage probe set comprising (i) a first cleavage probe comprising a sequence that is complementary to a first target region and (ii) a second cleavage probe comprising a sequence that is complementary to a second target region and that is downstream from a flap portion, wherein the second target region is located 5′ - of the first target region and overlaps the first target region by at least one nucleotide, under effective conditions for the first and second cleavage probes of the first cleavage probe set to anneal to the corresponding first and second target regions, respectively, forming a first hybridization complex;
(b) cleaving the flap portion of the second cleavage probe in the first hybridization complex to generate a cleaved flap and form a second hybridization complex comprising (1) the target sequence, (2) the first cleavage probe, and (3) an annealed fragment of the second cleavage probe having a 5′
-terminal nucleotide located adjacent to the 3′
-end of the annealed first cleavage probe;
(c) ligating the first cleavage probe to the annealed fragment of the second cleavage probe to generate a first ligation product and form a third hybridization complex comprising the target sequence and the first ligation product; and
(d) determining the degree of methylation of the target nucleotide. - View Dependent Claims (2, 3, 4, 5)
- of the first target region and overlaps the first target region by at least one nucleotide, under effective conditions for the first and second cleavage probes of the first cleavage probe set to anneal to the corresponding first and second target regions, respectively, forming a first hybridization complex;
-
6. A method for determining the degree of methylation of a target nucleotide comprising,
(a) reacting (1) a target sequence with (2) a first cleavage probe set comprising (i) a first cleavage probe that can hybridize with the target sequence and (ii) a second cleavage probe that (a) can hybridize with the target sequence downstream of the first cleavage probe and (b) contains a flap portion, under effective conditions for the first and second cleavage probes of the first cleavage probe set to hybridize with the target sequence, forming a first hybridization complex; -
(b) cleaving the flap portion of the second cleavage probe in the first hybridization complex to generate a cleaved flap and form a second hybridization complex comprising (1) the target sequence, (2) the first cleavage probe, and (3) an annealed fragment of the second cleavage probe having a 5′
-terminal nucleotide located adjacent to the 3′
-end of the annealed first cleavage probe;
(c) ligating the first cleavage probe to the annealed fragment of the second cleavage probe to generate a first ligation product and form a third hybridization complex comprising the target sequence and the first ligation product;
(d) denaturing the third hybridization complex;
(e) performing one or more additional cycles of steps (a) through (c) and optionally, step (d); and
(f) determining the degree of methylation of the target nucleotide. - View Dependent Claims (7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
-
-
20. A method for determining the degree of methylation of a target nucleotide, comprising:
-
a step for interrogating the target nucleotide;
a step for generating a cleaved flap;
a step for generating a ligation product; and
a step for determining the degree of methylation of the target nucleotide. - View Dependent Claims (18, 19)
-
Specification