Patents Assigned to New England Biolabs
  • High Fidelity Restriction Endonucleases
    Publication number: 20130115681
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Application
    Filed: January 8, 2013
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: New England Biolabs, Inc.
  • High Fidelity Restriction Endonucleases
    Publication number: 20130115679
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Application
    Filed: January 8, 2013
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: NEW ENGLAND BIOLABS, INC.
  • Method for Enriching Methylated CpG Sequences
    Publication number: 20130116409
    Abstract: Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.
    Type: Application
    Filed: December 20, 2012
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: New England Biolabs, Inc.
  • High Fidelity Restriction Endonucleases
    Publication number: 20130115680
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Application
    Filed: January 8, 2013
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: NEW ENGLAND BIOLABS, INC.
  • High Fidelity Restriction Endonucleases
    Publication number: 20130115677
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Application
    Filed: January 8, 2013
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: NEW ENGLAND BIOLABS, INC.
  • High Fidelity Restriction Endonucleases
    Publication number: 20130115676
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions includes restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Application
    Filed: January 8, 2013
    Publication date: May 9, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: NEW ENGLAND BIOLABS, INC.
  • Methods and Compositions for Detection and Enrichment of Target Small RNAs
    Publication number: 20130109018
    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: Application
    Filed: December 21, 2012
    Publication date: May 2, 2013
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: New England Biolabs, Inc.
  • High fidelity restriction endonucleases
    Patent number: 8372619
    Abstract: Compositions and methods are provided for enzymes with altered properties that involve a systematic approach to mutagenesis and a screening assay that permits selection of the desired proteins. Embodiments of the method are particularly suited for modifying specific properties of restriction endonucleases such as star activity. The compositions include restriction endonucleases with reduced star activity as defined by an overall fidelity index improvement factor.
    Type: Grant
    Filed: July 14, 2008
    Date of Patent: February 12, 2013
    Assignee: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Aine Blanchard, Shuang-Yong Xu, Shengxi Guan, Hua Wei, Penghua Zhang, Dapeng Sun, Siu-hong Chan
  • Method for enriching methylated CpG sequences
    Patent number: 8367331
    Abstract: Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.
    Type: Grant
    Filed: October 29, 2009
    Date of Patent: February 5, 2013
    Assignee: New England Biolabs, Inc.
    Inventors: George R. Feehery, Sriharsa Pradhan
  • Polynucleotides encoding polypeptides and host cells therefor
    Patent number: 8361773
    Abstract: Recombinant DNA encoding NruI- and SboI-like restriction endonucleases and methylases and their amino acid sequences are provided as well as methods for expressing the enzymes in transformed host cells and purifying the enzymes.
    Type: Grant
    Filed: March 30, 2007
    Date of Patent: January 29, 2013
    Assignee: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Jack S. Benner, II, Shuang-Yong Xu
  • rBSA from expression, secretion and purification of recombinant bovine serum albumin (rBSA) from and uses thereof
    Patent number: 8361750
    Abstract: A recombinant BSA (rBSA) that (a) substantially lacks deoxyribonuclease activity as determined by incubating rBSA with linear DNA overnight and gel electrophoresis, (b) lacks animal viruses associated with animal-derived cell growth supplements; and (c) is capable of stabilizing DNA proteins is provided. Methods for making the rBSA and using it to stabilize enzymes are also provided.
    Type: Grant
    Filed: March 30, 2007
    Date of Patent: January 29, 2013
    Assignee: New England Biolabs, Inc.
    Inventors: Paul A. Colussi, Thomas C. Evans, Jr., Christopher H. Taron
  • Recombinant type II restriction endonuclease, NmeAIII, and a process for producing the same
    Patent number: 8361774
    Abstract: A protein is described that has an amino acid sequence characterized by at least 90% sequence identity with SEQ ID NO: 24, the protein being capable of recognizing a sequence consisting of 5?-GCCGAG-3? within the double-stranded DNA and cleaving the substrate predominantly at 21/19 nucleotides from the recognition site. A method is also described that utilizes the protein for creating a DNA tag for use as a unique identifier for paired end sequencing of DNA or serial analysis of gene expression.
    Type: Grant
    Filed: December 21, 2007
    Date of Patent: January 29, 2013
    Assignee: New England Biolabs, Inc.
    Inventor: Richard D. Morgan
  • Compositions, Methods and Related Uses for Cleaving Modified DNA
    Publication number: 20120301881
    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: Application
    Filed: January 20, 2011
    Publication date: November 29, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Zhenyu Zhu, Yu Zheng, Shengxi Guan, Hua Wang, Aine Quimby, Penghua Zhang, Lynne Apone
  • Solubilized Phospholipids for Stabilizing Nucleic Acid Polymerases
    Publication number: 20120282669
    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: November 8, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Donald Johnson, Thomas C. Evans, JR.
  • Ligation Enhancement
    Publication number: 20120283144
    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: May 4, 2012
    Publication date: November 8, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Rebecca Kucera, Thomas C. Evans, JR.
  • Compositions and methods relating to elutable carbohydrate-binding proteins
    Patent number: 8288337
    Abstract: Compositions and methods are provided for creating and identifying mutant carbohydrate-binding proteins that reversibly bind to carbohydrate substrates under conditions where the native protein remains bound. Examples of modified chitin-binding domains are provided which can be eluted from chitin in the presence of a reducing agent or at a pH within the range of 5-10.
    Type: Grant
    Filed: March 6, 2009
    Date of Patent: October 16, 2012
    Assignee: New England Biolabs, Inc.
    Inventors: Christopher H. Taron, Paul A. Colussi, Jeremiah Read
  • Novel Restriction Endonucleases, DNA Encoding These Endonucleases and Methods for Identifying New Endonucleases with the Same or Varied Specificity
    Publication number: 20120254213
    Abstract: Specified restriction endonucleases have been characterized for the first time by their amino acid and DNA sequences. These sequences and those with at least 90% identity thereto have been used as probes in sequence similarity analyses to identify sequence matches in a sequence database that corresponds to novel restriction endonucleases or isoschizomers. The sequence similarity analyses includes selecting a positive sequence match from any sequence producing an expectation value of less than or equal to e?02.
    Type: Application
    Filed: June 6, 2012
    Publication date: October 4, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: Richard D. Morgan, Richard J. Roberts
  • Methods and Compositions for Enriching Either Target Polynucleotides or Non-Target Polynucleotides from a Mixture of Target and Non-Target Polynucleotides
    Publication number: 20120252009
    Abstract: Compositions and methods are provided for enriching non-target polynucleotides from a mixture of non-target and target polynucleotides where differences between the target polynucleotides and the non-target polynucleotides include the extent of modified bases that are present in a greater density in the target polynucleotides than in the non-target polynucleotides. This permits the target polynucleotides to be selectively and rapidly bound to an affinity matrix such as affinity protein-coated magnetic beads providing enrichment of the non-target polynucleotides in the supernatant. One use of this enrichment is to remove human genomic DNA from a mixture of DNAs obtained from human tissue samples to enrich for polynucleotides in a microbiome so as to characterize the microbiome by DNA sequencing.
    Type: Application
    Filed: March 30, 2012
    Publication date: October 4, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventors: George R. Feehery, Fiona Stewart, James McFarland, Sriharsa Pradhan
  • Oligonucleotide Adapters: Compositions and Methods of Use
    Publication number: 20120244525
    Abstract: Compositions are provided that include a synthetic oligonucleotide characterized by a double-stranded region, a single-stranded region, a forward primer site, a reverse primer site and one or more cleavage sites therebetween. Methods of use for these compositions include adapters for the amplification of DNA fragments.
    Type: Application
    Filed: June 5, 2012
    Publication date: September 27, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: Cynthia Hendrickson
  • Oligonucleotide Adapters: Compositions and Methods of Use
    Publication number: 20120238738
    Abstract: Compositions are provided that include a synthetic oligonucleotide characterized by a double-stranded region, a single-stranded region, a forward primer site, a reverse primer site and one or more cleavage sites therebetween. Methods of use for these compositions include adaptors for the amplification of DNA fragments.
    Type: Application
    Filed: June 13, 2011
    Publication date: September 20, 2012
    Applicant: NEW ENGLAND BIOLABS, INC.
    Inventor: Cynthia Hendrickson