Patents Assigned to New England Biolabs
  • Method for Reducing Adapter-Dimer Formation
    Publication number: 20150072870
    Abstract: Methods are provided for ligating a 3? adapter and a 5? adapter to a target polynucleotide so as to avoid adapter dimer formation. Embodiments of the methods include adding a blocking oligonucleotide after the first ligation in which a 3? adapter is ligated to the target polynucleotide so that the blocking oligonucleotide is capable of hybridizing to excess 3? adapter and the ligated 3? adapter. Subsequently, a 5? adapter is ligated to the target polynucleotide thus avoiding adapter dimer formation.
    Type: Application
    Filed: October 7, 2014
    Publication date: March 12, 2015
    Applicant: New England Biolabs, Inc.
    Inventors: Larry A. McReynolds, Daniela Munafo
  • Compositions, methods and related uses for cleaving modified DNA
    Patent number: 8969061
    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.
    Type: Grant
    Filed: January 20, 2011
    Date of Patent: March 3, 2015
    Assignee: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Yu Zheng, Shengxi Guan, Hua Wang, Aine Quimby, Penghua Zhang, Lynne Apone
  • Endoglycosidases that cleave -linked glycans
    Patent number: 8969034
    Abstract: Methods and compositions have been described that relate to a newly identified polypeptide family wherein each member has O-glycosidase activity and specified sequence characteristics. This family of enzymes can be used for example for cleaving O-linked glycans and for synthesis of neoglycopeptides or neoglycoproteins.
    Type: Grant
    Filed: April 7, 2009
    Date of Patent: March 3, 2015
    Assignee: New England Biolabs, Inc.
    Inventors: Dimitris Koutsioulis, Ellen Guthrie
  • Composition, Method and Kit for Obtaining Purified Recombinant Proteins
    Publication number: 20150037866
    Abstract: Compositions relating to a combination of two types of separation matrix; and to variant host cells which contain at least one essential host protein that is fused to an affinity binding tag or has been mutated to replace at least two of a plurality of histidines or basic amino acids are provided. Methods are also provided that relate to isolating a recombinant protein from a lysate.
    Type: Application
    Filed: August 26, 2011
    Publication date: February 5, 2015
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: James C. Samuelson, Carine Robichon-Iyer, Jianying Luo
  • DNA polymerase variants with reduced exonuclease activity and uses thereof
    Patent number: 8921043
    Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.
    Type: Grant
    Filed: May 10, 2012
    Date of Patent: December 30, 2014
    Assignee: New England Biolabs, Inc.
    Inventor: Andrew Gardner
  • DNA polymerase variants with reduced exonuclease activity and uses thereof
    Patent number: 8921044
    Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.
    Type: Grant
    Filed: April 8, 2014
    Date of Patent: December 30, 2014
    Assignee: New England BioLabs, Inc.
    Inventor: Andrew Gardner
  • Solubilized phospholipids for stabilizing nucleic acid polymerases
    Patent number: 8883474
    Abstract: Compositions and methods are provided that relate to solubilized phospholipids and their use in stabilizing nucleic acid polymerases. For example, a phospholipid with a tail containing at least 8 carbons can be solubilized in the presence of an amphipathic molecule.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: November 11, 2014
    Assignee: New England Biolabs, Inc
    Inventors: Donald Johnson, Thomas C. Evans
  • Asymmetric adapter library construction
    Patent number: 8883990
    Abstract: The present invention provides methods and compositions for asymmetrically tagging a nucleic acid fragment using asymmetric adapters.
    Type: Grant
    Filed: March 11, 2013
    Date of Patent: November 11, 2014
    Assignee: New England Biolabs, Inc.
    Inventor: Gi Mikawa
  • Method for reducing adapter-dimer formation
    Patent number: 8883421
    Abstract: Methods are provided for ligating a 3? adapter and a 5? adapter to a target polynucleotide so as to avoid adapter dimer formation. Embodiments of the methods include adding a blocking oligonucleotide after the first ligation in which a 3? adapter is ligated to the target polynucleotide so that the blocking oligonucleotide is capable of hybridizing to excess 3? adapter and the ligated 3? adapter. Subsequently, a 5? adapter is ligated to the target polynucleotide thus avoiding adapter dimer formation.
    Type: Grant
    Filed: August 31, 2011
    Date of Patent: November 11, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Larry A. McReynolds, Daniela Munafo
  • DNA Polymerase Variants with Reduced Exonuclease Activity and Uses Thereof
    Publication number: 20140296082
    Abstract: Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo?” polymerases, and a sensitive screening assay that enables an assessment of exonuclease activity of any synthetic DNA polymerase.
    Type: Application
    Filed: April 8, 2014
    Publication date: October 2, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: Andrew Gardner
  • COMPOSITIONS, METHODS AND RELATED USES FOR CLEAVING MODIFIED DNA
    Publication number: 20140194299
    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.
    Type: Application
    Filed: January 30, 2014
    Publication date: July 10, 2014
    Applicant: New England Biolabs, Inc.
    Inventors: YU ZHENG, RICHARD J. ROBERTS
  • Ligation Enhancement
    Publication number: 20140187447
    Abstract: Compositions and methods are provided for enhancing enzymatic ligation between nucleic acid fragments that relies on one or more small molecule enhancers having a size of less than 1000 daltons. For example, enhancement of ligation efficiencies are observed for double-stranded nucleic acid fragments that are blunt-ended, have a single nucleotide overhang at the ligation end, or have staggered ends compared to ligation under similar conditions in the absence of the one or more small molecule ligation enhancer. The use of small molecule enhancers for ligating nucleic acids results in an increased number of transformed host cells after transformation with the ligated molecules. This enhancement can be observed with chemically transformed host cells and with host cells transformed by electroporation.
    Type: Application
    Filed: February 26, 2014
    Publication date: July 3, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Rebecca Kucera, Thomas C. Evans, JR.
  • Novel Ligase Activity
    Publication number: 20140179539
    Abstract: Compositions and methods are provided for ligating polynucleotides having a length that is greater than 8 nucleotides on an RNA splint. The ligation reaction provides consistent results in high or low ATP concentrations. The reaction can occur rapidly and is generally at least 10 fold more efficient than T4DNA ligase under optimal conditions for T4DNA ligase and the reaction time is less than 6 hours for example, less than 1 hour.
    Type: Application
    Filed: March 14, 2013
    Publication date: June 26, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Gregory Lohman, Thomas C. Evans
  • Methods and compositions for detection and enrichment of target small RNAs
    Patent number: 8753809
    Abstract: Methods and compositions are provided for detecting small target RNAs where the target RNA may be single-stranded or double-stranded and may be contained in a mixture of RNAs of different types and sizes. The methods and compositions utilize a p19 fusion protein that is capable of binding double-stranded RNA in a size-specific but sequence-independent manner and is further capable of binding to a matrix such as beads or plastic microwell plates. By labeling the p19 fusion protein or the target RNA in a polynucleotide duplex either directly or indirectly, low levels of target RNA including microRNAs can be detected from cells. This can be applied to diagnosis of pathological conditions.
    Type: Grant
    Filed: December 21, 2012
    Date of Patent: June 17, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Larry A. McReynolds, Jingmin Jin
  • Selection and enrichment of proteins using in vitro compartmentalization
    Patent number: 8753847
    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.
    Type: Grant
    Filed: August 13, 2013
    Date of Patent: June 17, 2014
    Assignee: New England Biolabs, Inc.
    Inventors: Yu Zheng, Richard J. Roberts
  • High Fidelity Restriction Endonucleases
    Publication number: 20140154779
    Abstract: Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 5, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Zhenyu Zhu, Aine Quimby, Shengxi Guan, Dapeng Sun, Yishu Huang, Xuhui Lai, Siu-hong Chan, Xianghui Li, Shuang-Yong Xu, Chunhua Zhang
  • High Fidelity Restriction Endonucleases
    Publication number: 20140154778
    Abstract: Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 5, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Zhenyu Zhu, Aine Quimby, Shengxi Guan, Dapeng Sun, Yishu Huang, Xuhui Lai, Siu-hong Chan, Xianghui Li, Shuang-Yong Xu, Chunhua Zhang
  • High Fidelity Restriction Endonucleases
    Publication number: 20140154780
    Abstract: Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 5, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Zhenyu Zhu, Aine Quimby, Shengxi Guan, Dapeng Sun, Yishu Huang, Xuhui Lai, Siu-hong Chan, Xianghui Li, Shuang-Yong Xu, Chunhua Zhang
  • High Fidelity Restriction Endonucleases
    Publication number: 20140154676
    Abstract: Methods and compositions are provided for engineering mutant enzymes with reduced star activity where the mutant enzymes have a fidelity index (FI) in a specified buffer that is greater than the FI of the non-mutated enzyme in the same buffer.
    Type: Application
    Filed: December 20, 2013
    Publication date: June 5, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Zhenyu Zhu, Aine Quimby, Shengxi Guan, Dapeng Sun, Yishu Huang, Xuhui Lai, Siu-hong Chan, Xianghui Li, Shuang-Yong Xu, Chunhua Zhang
  • Solubilized Phospholipids for Stabilizing Nucleic Acid Polymerases
    Publication number: 20140134702
    Abstract: Compositions and methods are provided that relate to solubilized phospholipids and their use in stabilizing nucleic acid polymerases. For example, a phospholipid with a tail containing at least 8 carbons can be solubilized in the presence of an amphipathic molecule.
    Type: Application
    Filed: April 19, 2012
    Publication date: May 15, 2014
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Donald Johnson, Thomas C. Evans, JR.