Methylation analysis using nicking agents
First Claim
Patent Images
1. A method for characterizing the methylation state of a target nucleic acid, comprising:
- a. treating the target nucleic acid with a modifying agent that differentially modifies a nucleotide based on the methylation state of the nucleotide to provide a treated target nucleic acid;
b. providing a template double-stranded nucleic acid that comprises a nicking agent recognition sequence (NARS) and a portion of the treated target nucleic acid or an amplification product thereof if the target nucleic acid is single-stranded or a portion of one strand of the treated target nucleic acid if the target nucleic acid is double-stranded;
c. amplifying a single-stranded nucleic acid fragment in the presence of a nicking agent (NA) that recognizes the NARS, a DNA polymerase, and one or more deoxynucleoside triphosphate(s), wherein the amplifying uses a portion of the template double-stranded nucleic acid as a template, wherein the single-stranded nucleic acid fragment contains no more than 20 nucleotides; and
d. characterizing the single-stranded nucleic acid fragment and thereby characterizing the methylation state of the target nucleic acid.
1 Assignment
0 Petitions
Accused Products
Abstract
The present invention provides methods and compositions for nucleic acid methylation analysis using nicking agents.
113 Citations
49 Claims
-
1. A method for characterizing the methylation state of a target nucleic acid, comprising:
-
a. treating the target nucleic acid with a modifying agent that differentially modifies a nucleotide based on the methylation state of the nucleotide to provide a treated target nucleic acid;
b. providing a template double-stranded nucleic acid that comprises a nicking agent recognition sequence (NARS) and a portion of the treated target nucleic acid or an amplification product thereof if the target nucleic acid is single-stranded or a portion of one strand of the treated target nucleic acid if the target nucleic acid is double-stranded;
c. amplifying a single-stranded nucleic acid fragment in the presence of a nicking agent (NA) that recognizes the NARS, a DNA polymerase, and one or more deoxynucleoside triphosphate(s), wherein the amplifying uses a portion of the template double-stranded nucleic acid as a template, wherein the single-stranded nucleic acid fragment contains no more than 20 nucleotides; and
d. characterizing the single-stranded nucleic acid fragment and thereby characterizing the methylation state of the target nucleic acid. - 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. A method for the multiplex characterization of methylation states of at least portions of target nucleic acids, comprising
a. treating the target nucleic acids with a modifying agent that differentially modifies a nucleotide based on the methylation state of the nucleotide, to provide treated target nucleic acids; -
b. for each target nucleic acid, providing a template double-stranded nucleic acid that comprises a nicking agent recognition sequence (NARS) and a portion of the treated target nucleic acid or an amplification product thereof;
c. amplifying single-stranded nucleic acid fragments in the presence of a nicking agent (NA) that recognizes the NARS, a DNA polymerase, and one or more deoxynucloside triphosphate(s), wherein the amplifying uses a portion of each template double-stranded nucleic acid as a template, wherein the single-stranded nucleic acid fragments each contains no more than 20 nucleotides; and
d. characterizing the single-stranded nucleic acid fragments and thereby characterizing the methylation state of at least portions of the target nucleic acids. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43)
-
-
44. A method for characterizing the methylation state of a target nucleic acid, comprising:
-
a. treating the target nucleic acid with a modifying agent that differentially modifies a nucleotide based on the methylation state of the nucleotide to provide a treated target nucleic acid;
b. providing a first template double-stranded nucleic acid that comprises a nicking agent recognition sequence (NARS) and a portion of the treated target nucleic acid or an amplification product thereof if the target nucleic acid is single-stranded or a portion of one strand of the treated target nucleic acid if the target nucleic acid is double-stranded;
c. providing a second template double-stranded nucleic acid that comprises the NARS and a portion of untreated target nucleic acid or an amplification product thereof if the target nucleic acid is single-stranded or a portion of one strand of the untreated target nucleic acid if the target nucleic acid is double-stranded;
d. amplifying a first single-stranded nucleic acid fragment in the presence of a nicking agent (NA) that recognizes the NARS, a DNA polymerase, and one or more deoxynucleoside triphosphate(s), wherein the amplifying uses a portion of the first template double-stranded nucleic acid as a template, wherein the first single-stranded nucleic acid fragment contains no more than 20 nucleotides;
e. amplifying a second single-stranded nucleic acid fragment in the presence of of the NA, the DNA polymerase and the deoxynucleoside triphosphate(s), wherein the amplifying uses a portion of the second template double-stranded nucleic acid as a template, wherein the second single-stranded nucleic acid fragment contains no more than 20 nucleotides;
f. characterizing the first single-stranded nucleic acid fragment;
g. characterizing the second single-stranded nucleic acid fragment; and
h. comparing the characteristic of the first single-straned nucleic acid fragment obtained from step (f) with the characteristic of the second single-stranded nucleic acid fragment obtained from step (g), and thereby characterizing the methylation state of the target nucleic acid. - View Dependent Claims (45, 46, 47, 48, 49)
-
Specification