Methods for analysis of nucleic acid methylation status and methods for fragmentation, labeling and immobilization of nucleic acids
First Claim
Patent Images
1. A method for fragmenting a polynucleotide comprising a methylated nucleotide and an unmethylated nucleotide, said method comprising:
- (a) mixing the polynucleotide with a methyl binding protein thereby forming a complex comprising the polynucleotide and the methyl binding protein;
(b) cleaving a base portion of the unmethylated nucleotide of the polynucleotide in the complex with an agent capable of cleaving a base portion of an unmethylated nucleotide, whereby an abasic site is generated in the polynucleotide of the complex and wherein the methyl binding protein binds to the methylated nucleotide of the polynucleotide in the complex so that the agent is not capable of cleaving a base portion of the methylated nucleotide of the polynucleotide in the complex; and
(c) fragmenting the phosphodiester backbone of the polynucleotide of the complex at the abasic site, whereby polynucleotide fragments are generated, wherein said fragmenting the phosphodiester backbone is performed with an amine, wherein the amine is N,N′
-dimethylethylenediamine.
3 Assignments
0 Petitions
Accused Products
Abstract
The invention relates to methods for analysis of nucleic acid methylation status, and fragmentation and/or labeling and/or immobilization of nucleic acids. More particularly, the invention relates to methods for fragmentation and/or labeling and/or immobilization of nucleic acids comprising labeling and/or cleavage and/or immobilization at abasic sites.
134 Citations
22 Claims
-
1. A method for fragmenting a polynucleotide comprising a methylated nucleotide and an unmethylated nucleotide, said method comprising:
-
(a) mixing the polynucleotide with a methyl binding protein thereby forming a complex comprising the polynucleotide and the methyl binding protein; (b) cleaving a base portion of the unmethylated nucleotide of the polynucleotide in the complex with an agent capable of cleaving a base portion of an unmethylated nucleotide, whereby an abasic site is generated in the polynucleotide of the complex and wherein the methyl binding protein binds to the methylated nucleotide of the polynucleotide in the complex so that the agent is not capable of cleaving a base portion of the methylated nucleotide of the polynucleotide in the complex; and (c) fragmenting the phosphodiester backbone of the polynucleotide of the complex at the abasic site, whereby polynucleotide fragments are generated, wherein said fragmenting the phosphodiester backbone is performed with an amine, wherein the amine is N,N′
-dimethylethylenediamine. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
-
-
18. A method of capturing a methylated portion of a polynucleotide that comprises a methylated nucleotide and an unmethylated nucleotide, the method comprising:
-
(a) treating the polynucleotide with a methyl binding protein thereby forming a complex comprising the polynucleotide and the methyl binding protein, wherein the methyl binding protein binds to the methylated nucleotide of the polynucleotide in the complex; (b) cleaving a base portion of an unmethylated nucleotide with an agent capable of cleaving a base portion of an unmethylated nucleotide in a portion of the polynucleotide not bound to the methyl binding agent, whereby an abasic site in the polynucleotide of the complex is generated; (c) fragmenting the phosphodiester backbone at the abasic site of the polynucleotide, whereby polynucleotide fragments are generated, wherein said fragmenting the phosphodiester backbone is performed with an amine, wherein the amine is N,N′
dimethylethylenediamine; and(d) capturing polynucleotide fragments comprising the methylated nucleotide from the polynucleotide fragments generated in step (c). - View Dependent Claims (19, 20, 21, 22)
-
Specification