Yu Zheng

US Patent:

8153358, Apr 10, 2012

Filed:

Feb 22, 2008

Appl. No.:

12/035872

Inventors:

Yu Zheng - Melrose MA, US
Richard J. Roberts - Wenham MA, US

Assignee:

New England Biolabs, Inc. - Ipswich MA

International Classification:

C12Q 1/00
C12Q 1/68
C12P 21/06

US Classification:

435 4, 435 61, 435 691

Abstract:

Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.

US Patent:

8551734, Oct 8, 2013

Filed:

Mar 8, 2012

Appl. No.:

13/415504

Inventors:

Yu Zheng - Topsfield MA, US
Richard J. Roberts - Wenham MA, US

International Classification:

C12P 21/06
C12Q 1/68
G01N 33/573
C12P 19/34
C12N 9/00

US Classification:

435 691, 435 74, 435 618, 435 612, 435 911, 435 912, 435 915, 435 9152, 435183

Abstract:

Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.

US Patent:

20100167942, Jul 1, 2010

Filed:

Dec 22, 2009

Appl. No.:

12/644666

Inventors:

Yu Zheng - Topsfield MA, US
Richard J. Roberts - Wenham MA, US

Assignee:

NEW ENGLAND BIOLABS, INC. - Ipswich MA

International Classification:

C40B 30/02
C40B 40/06
C40B 40/08
C12N 9/16
C07K 16/00
C12P 19/34
C12Q 1/68

US Classification:

506 8, 506 16, 506 17, 435196, 5303871, 435 9153, 435 6

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)YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.

US Patent:

20120156677, Jun 21, 2012

Filed:

Aug 25, 2010

Appl. No.:

13/392286

Inventors:

Jurate Bitinaite - Rowley MA, US
Romualdas Vaisvila - Ipswich MA, US
Sriharsa Pradhan - Wenham MA, US
Yu Zheng - Topsfield MA, US
Richard J. Roberts - Wenham MA, US
Christopher Noren - Boxford MA, US
Elisabeth A. Raleigh - Somerville MA, US
Geoffrey Wilson - South Hamilton MA, US

Assignee:

NEW ENGLAND BIOLABS, INC. - Ipswich MA

International Classification:

C12Q 1/68

US Classification:

435 611

Abstract:

Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.

US Patent:

20120202712, Aug 9, 2012

Filed:

Apr 6, 2012

Appl. No.:

13/441208

Inventors:

Yu Zheng - Topsfield MA, US
Richard J. Roberts - Wenham MA, US

Assignee:

NEW ENGLAND BIOLABS, INC. - Ipswich MA

International Classification:

C40B 40/06

US Classification:

506 16

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)YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.

US Patent:

20120301881, Nov 29, 2012

Filed:

Jan 20, 2011

Appl. No.:

13/522224

Inventors:

Zhenyu Zhu - Beverly MA, US
Yu Zheng - Topsfield MA, US
Shengxi Guan - Stoneham MA, US
Hua Wang - Topsfield MA, US
Aine Quimby - Newton NH, US
Penghua Zhang - Lexington MA, US
Lynne Apone - Waltham MA, US

Assignee:

NEW ENGLAND BIOLABS, INC. - Ipswich MA

International Classification:

C12Q 1/68
C12N 9/16

US Classification:

435 611, 435196

Abstract:

Compositions, methods and a kit are described relating to a novel family of enzymes which preferentially bind to a hydroxymethylated cytosine or a glucosylated hydroxymethylated cytosine and cleave double-stranded DNA at a defined distance 3′ of the recognition site to produce a cleavage fragment with a 1-3 base overhang.

US Patent:

20150240310, Aug 27, 2015

Filed:

Apr 14, 2015

Appl. No.:

14/685966

Inventors:

- Ipswich MA, US
Romualdas Vaisvila - Ipswich MA, US
Sriharsa Pradhan - Wenham MA, US
Yu Zheng - Topsfield MA, US
Richard J. Roberts - Wenham MA, US
Christopher Noren - Boxford MA, US
Elisabeth A. Raleigh - Somerville MA, US
Geoffrey Wilson - South Hamilton MA, US

Assignee:

NEW ENGLAND BIOLABS, INC. - Ipswich MA

International Classification:

C12Q 1/68

Abstract:

Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.