Mapping cytosine modifications

• US 9,267,117 B2
• Filed: 03/14/2013
• Issued: 02/23/2016
• Est. Priority Date: 03/15/2012
• Status: Active Grant

• Current Assignee: New England Biolabs Incorporated
• Original Assignee: New England Biolabs Incorporated
• Inventors: Guan, Shengxi, Dai, Nan, Zhu, Zhenyu, Correa, Ivan R. Jr., Quimby, Aine, Borgaro, Janine
• Primary Examiner(s): NASHED, NASHAAT T
• Application Number:
  US13/826,395
• Publication Number:
  US 20140127678A1
• Time in Patent Office: 1,076 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 2319/80 containing a DNA binding domain, e.g. Lacl or Tet-repressor
• CPC Class Codes: C07K 2319/81 containing a Zn-finger domain for DNA binding
• CPC Class Codes: C12N 9/0069 acting on single donors with incorporation of molecular oxygen, i.e. oxygenases (1.13)
• CPC Class Codes: C12N 9/1051 Hexosyltransferases (2.4.1)
• CPC Class Codes: C12N 9/22 Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113
• CPC Class Codes: C12P 19/18 produced by the action of a glycosyl transferase, e.g. alpha-, beta- or gamma-cyclodextrins
• CPC Class Codes: C12P 19/30 Nucleotides
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2523/115 oxidising agents
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2537/164 : Methylation detection other then bisulfite or methylation sensitive restriction endonucleases
• CPC Class Codes: Y02P 20/52 : using catalysts, e.g. selective catalysts

Abstract

Methods, compositions and kits for selectively altering and detecting modified cytosine residues are provided.

Claims

1. A composition comprising a reducing agent capable of converting 5-formylcytosine or 5-carboxycytosine to 5-hydroxymethylcytosine;

T4 β

-glucosyltransferase (BGT) and a UDP derivative selected from the group consisting of UDP-glucose and UDP-azidoglucose.

2. A composition according to claim 1, further comprising a nucleic acid.

3. A kit comprising a reducing agent capable of converting 5-formylcytosine or 5-carboxycytosine to 5-hydroxymethylcytosine;

T4 β

-glucosyltransferase (BGT); and

a UDP derivative selected from the group consisting of UDP-glucose and UDP-azidoglucose.

4. A kit according to claim 3, further comprising UDP-glucosamine.

5. A kit according to claim 3, further comprising a nucleic acid.

6. A kit according to any claim 3, further comprising an oxidizing agent that is capable of oxidizing 5-methylcytosine to 5-hydroxymethylcytosine.