Compositions, Methods and Related Uses for Cleaving Modified DNA
First Claim
1. A set of double-stranded oligonucleotide fragments obtainable by enzymatic cleavage of a large DNA, the large DNA containing one or more modified nucleotides, the set comprising fragments wherein at least 50% are of a similar size and have a centrally positioned modified nucleotide.
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Abstract
Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X)10YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.
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Citations
41 Claims
- 1. A set of double-stranded oligonucleotide fragments obtainable by enzymatic cleavage of a large DNA, the large DNA containing one or more modified nucleotides, the set comprising fragments wherein at least 50% are of a similar size and have a centrally positioned modified nucleotide.
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23. An enzyme preparation, comprising:
- one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide, the one or more enzymes further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology with WXD(X)10YXGD.
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37. A method for obtaining a purified preparation of fragments containing one or more modified nucleotides, comprising:
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a. contacting a mixture of DNA fragments in which one or more of the fragments contain at least one modified nucleotide with an immobilized preparation of an affinity-binding molecule; b. binding the one or more fragments containing at least one modified nucleotide to the affinity-binding molecule; and c. obtaining a purified preparation of fragments containing one or more modified nucleotides.
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Specification