Patents Assigned to New England Biolabs, Inc.
  • Proteinases with Improved Properties
    Publication number: 20200199565
    Abstract: Provided herein is a thermolabile proteinase and methods of using the same. In some embodiments, the thermolabile proteinase may comprise an amino acid sequence that is at least 90% identical to any of SEQ ID NOs:1-11 and at least one amino acid substitution in helix 3. The thermolabile proteinase is active at a temperature in the range of 4° C.-40° C. and is inactivated by raising the temperature to above 50° C., where the proteinase is substantially inactive at 65° C.
    Type: Application
    Filed: December 18, 2019
    Publication date: June 25, 2020
    Applicant: New England Biolabs, Inc.
    Inventors: Minyong Chen, James C. Samuelson, Ming-Qun Xu, Aihua Zhang, Margaret Heider, Pingfang Liu
  • Target Enrichment
    Publication number: 20200199577
    Abstract: The present disclosure provides, among other things, a way to amplify and sequence target sequences in a low-input sample. In some embodiments, the method comprises ligating a double-stranded adaptor onto a population of fragments to produce tagged fragments, and linearly amplifying the tagged fragments.
    Type: Application
    Filed: December 19, 2019
    Publication date: June 25, 2020
    Applicant: New England Biolabs, Inc.
    Inventors: Cynthia Hendrickson, Sarah Bowman, Amy Emerman, Kruti Patel
  • Proteinases with improved properties
    Patent number: 10633644
    Abstract: Provided herein is a thermolabile proteinase and methods of using the same. In some embodiments, the thermolabile proteinase may comprise an amino acid sequence that is at least 90% identical to any of SEQ ID NOs:1-11 and at least one amino acid substitution in helix 3. The thermolabile proteinase is active at a temperature in the range of 4° C.-40° C. and is inactivated by raising the temperature to above 50° C., where the proteinase is substantially inactive at 65° C.
    Type: Grant
    Filed: December 18, 2019
    Date of Patent: April 28, 2020
    Assignee: New England Biolabs, Inc.
    Inventors: Minyong Chen, James C. Samuelson, Ming-Qun Xu, Aihua Zhang, Margaret Heider, Pingfang Liu
  • Thermostable Variants of T7 RNA Polymerase
    Publication number: 20200123513
    Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.
    Type: Application
    Filed: November 11, 2019
    Publication date: April 23, 2020
    Applicant: New England Biolabs, Inc.
    Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
  • Compositions and methods for analyzing modified nucleotides
    Patent number: 10619200
    Abstract: A method for identifying the location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and optionally reacting a second portion of the sample with a dioxygenase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase that is more efficient at converting methylcytosine to carboxymethylcytosine is also provided.
    Type: Grant
    Filed: October 28, 2016
    Date of Patent: April 14, 2020
    Assignee: New England Biolabs, Inc.
    Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
  • Methods and Compositions for Increasing Capping Efficiency of Transcribed RNA
    Publication number: 20200109425
    Abstract: Methods and compositions for capping RNA in an in vitro transcription mixture are provided that include a thermostable RNA polymerase variant and a cap analog such that when a DNA template is added to the mixture, and the mixture is then incubated under conditions for in vitro transcription, capped RNA is produced.
    Type: Application
    Filed: October 4, 2018
    Publication date: April 9, 2020
    Applicant: New England Biolabs, Inc.
    Inventors: Bijoyita Roy, Jennifer Ong
  • Ligase activity
    Patent number: 10597650
    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: Grant
    Filed: March 14, 2013
    Date of Patent: March 24, 2020
    Assignee: New England Biolabs, Inc.
    Inventors: Gregory Lohman, Thomas C. Evans, Larry A. McReynolds
  • Compositions and methods for identifying hydroxymethylcytosine in a DNA
    Patent number: 10597647
    Abstract: Provided herein in some embodiments is a non-naturally occurring variant of a wild type restriction enzyme defined by SEQ ID NO: 20, wherein the variant has at least a 2 fold increase in cleavage at 5-? glucosylhydroxymethylcytosine (5?ghmC) compared with methylcytosine relative to the wild type enzyme. Methods for examining hydroxymethylation of a DNA sample using the variant enzyme are also provided.
    Type: Grant
    Filed: June 27, 2014
    Date of Patent: March 24, 2020
    Assignee: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Janine Borgaro, Aine Quimby, Shengxi Guan, Zhiyi Sun
  • Ligase activity
    Patent number: 10597710
    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: Grant
    Filed: August 28, 2015
    Date of Patent: March 24, 2020
    Assignee: New England Biolabs, Inc.
    Inventors: Gregory Lohman, Thomas C. Evans, Jr., Larry A. McReynolds
  • High Fidelity Restriction Endonucleases
    Publication number: 20200063121
    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: September 11, 2019
    Publication date: February 27, 2020
    Applicant: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Aine Quimby, Shuang-Yong Xu, Shengxi Guan, Hua Wei, Penghua Zhang, Dapeng Sun, Siu-hong Chan
  • Thermostable variants of T7 RNA polymerase
    Patent number: 10519431
    Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.
    Type: Grant
    Filed: May 12, 2017
    Date of Patent: December 31, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
  • Universal N-glycan binding reagent
    Patent number: 10507233
    Abstract: Methods of capturing N-glycan linked glycomolecules including N-glycans, N-glycopeptides and N-glycoproteins are described. The methods provide substantially unbiased capture of charged and uncharged N-glycans and/or N-glycan linked glycomoleules. Binding reagents for substantially unbiased binding of N-glycans and/or N-glycan linked glycomolecules are also described.
    Type: Grant
    Filed: August 20, 2018
    Date of Patent: December 17, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Minyong Chen, Xiaofeng Shi, James C. Samuelson, Christopher H. Taron
  • Stabilizing 5?-flap endonuclease activity
    Patent number: 10487317
    Abstract: A probe qPCR master mix is provided. In some embodiments, the master mix comprises nucleotides, an enzyme comprising a polymerase activity and a flap endonuclease activity, a chelating agent at a concentration greater than 5 ?M, and a divalent cation. The relatively high concentration of chelating agent stabilizes the flap endonuclease activity during storage. As such, the polymerase and flap endonuclease activities may be substantially the same before and after storing the master mix for 7 days at 37° C.
    Type: Grant
    Filed: March 23, 2017
    Date of Patent: November 26, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Nicole Nichols, Gregory Patton, Janine Graham
  • High fidelity restriction endonucleases
    Patent number: 10450559
    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: Grant
    Filed: January 29, 2018
    Date of Patent: October 22, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Zhenyu Zhu, Aine Quimby, Shuang-Yong Xu, Shengxi Guan, Hua Wei, Penghua Zhang, Dapeng Sun, Siu-hong Chan
  • Methods for enriching for a population of RNA molecules
    Patent number: 10428368
    Abstract: A method of enriching for a population of RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding an affinity tag to the 5? end of 5?-diphosphorylated or 5?-triphosphorylated RNA molecules in a sample by incubating the sample with an affinity tag-labeled GTP and a capping enzyme; and (b) enriching for RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag.
    Type: Grant
    Filed: April 25, 2016
    Date of Patent: October 1, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, Jr., Michael Sproviero
  • High Fidelity Restriction Endonucleases
    Publication number: 20190276811
    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: March 15, 2019
    Publication date: September 12, 2019
    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 Throughput Reaction Assembly
    Publication number: 20190270975
    Abstract: Provided herein is a reverse transcriptase mixture comprising a reverse transcriptase and a colored dye at a concentration in the range of 0.003%-1% (v/w). The colored dye may be visually observed during transfer of the mix from one vessel to another and addition of the mix to another mix can be confirmed by eye by observing the colored dye.
    Type: Application
    Filed: February 26, 2019
    Publication date: September 5, 2019
    Applicant: New England Biolabs, Inc.
    Inventors: Guoping Ren, Yan Xu, Dong Ma, Nicole Nichols
  • Compositions and Methods Relating to Synthetic RNA Polynucleotides Created From Synthetic DNA Oligonucleotides
    Publication number: 20190225961
    Abstract: Compositions and methods are provided for forming a single RNA polynucleotide from a plurality of DNA oligonucleotides in a single reaction chamber using combined reagents in a single step reaction.
    Type: Application
    Filed: April 4, 2019
    Publication date: July 25, 2019
    Applicant: New England Biolabs, Inc.
    Inventors: G. B. Robb, Isaac B. Meek, Dianne S. Schwarz, Ezra Schildkraut
  • Analysis of Chromatin Using a Nicking Enzyme
    Publication number: 20190211404
    Abstract: Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.
    Type: Application
    Filed: August 31, 2017
    Publication date: July 11, 2019
    Applicant: New England Biolabs, Inc.
    Inventors: Chaithanya Ponnaluri, Hang-Gyeong Chin, Pierre O. Esteve, Sriharsa Pradhan
  • Compositions and Methods for Analyzing Modified Nucleotides
    Publication number: 20190185919
    Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA.
    Type: Application
    Filed: February 27, 2019
    Publication date: June 20, 2019
    Applicant: New England Biolabs, Inc.
    Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh