Patent ID: 8143001

Claim:
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.