Patents by Inventor Laurence Ettwiller
Laurence Ettwiller has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20240158833Abstract: Compositions, methods and kits are provided that describe a novel enzyme family called here a hydroxymethylcytosine carbamoyltransferase that transfers a carbamoyl phosphate substrate onto a hydroxymethylcytosine nucleoside triphosphate or a hydroxymethylcytosine in a nucleic acid. The carbamoyl phosphate substrate may be tagged with a chemically reactive group and optionally a functional group. This enables multiple uses of this enzyme and substrate for detecting nucleic acids with modified nucleotides, enriching for such nucleic acids, sequencing nucleic acids containing modified nucleotides, and for synthesizing oligonucleotides with various labels for various molecular biology applications including stabilizing RNA.Type: ApplicationFiled: February 17, 2022Publication date: May 16, 2024Applicant: New England Biolabs, Inc.Inventors: Laurence Ettwiller, Peter R. Weigele, Weiwei Yang, Yan-Jiun Lee, Ivan R. Correa, Jr.
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Patent number: 11939628Abstract: 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. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: GrantFiled: February 22, 2021Date of Patent: March 26, 2024Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Patent number: 11713484Abstract: Providing herein, among other things, is a method comprising incubating a double-stranded nucleic acid having a nick with a nick translating activity, a ligase, and a nucleotide mix comprising at least one modified nucleotide, to generate a product comprising a patch of a newly synthesized strand of a duplex nucleic acid containing a plurality of modified nucleoside monophosphates that are at or adjacent to the site of the nick. In some embodiments, the method may be used to map damaged nucleoside monophosphates in a nucleic acid. Compositions and kits for use in performing the method are also provided.Type: GrantFiled: August 21, 2018Date of Patent: August 1, 2023Inventors: Kelly M. Zatopek, Vladimir Potapov, Jennifer Ong, Laurence Ettwiller, Lixin Chen, Thomas C. Evans, Jr., Andrew F. Gardner
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Publication number: 20230022745Abstract: A method of labeling, and optionally enriching, for a population of target RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding a label to the 5? end of 5?-diphosphorylated or 5?-triphosphorylated target RNA molecules in a sample by incubating the sample with labeled GTP and a capping enzyme; and (b) optionally enriching for target RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag. The label may be an oligonucleotide, which may further comprise an affinity group attached either internally or at 5? or 3? end of the oligonucleotide where the oligonucleotide label may be added directly, or indirectly via a reaction with a reactive group to the target RNA.Type: ApplicationFiled: September 14, 2022Publication date: January 26, 2023Applicant: New England Biolabs, Inc.Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, JR., George Tzertzinis, John Buswell, Madalee G. Wulf
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Patent number: 11479766Abstract: A method of labeling, and optionally enriching, for a population of target RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding a label to the 5? end of 5?-diphosphorylated or 5?-triphosphorylated target RNA molecules in a sample by incubating the sample with labeled GTP and a capping enzyme; and (b) optionally enriching for target RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag. The label may be an oligonucleotide, which may further comprise an affinity group attached either internally or at 5? or 3? end of the oligonucleotide where the oligonucleotide label may be added directly, or indirectly via a reaction with a reactive group to the target RNA.Type: GrantFiled: February 28, 2018Date of Patent: October 25, 2022Assignee: New England Biolabs, Inc.Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, Jr., George Tzertzinis, John Buswell, Madalee G. Wulf
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Patent number: 11225658Abstract: Provided herein is a method for making an cDNA library, comprising adding an affinity tag-labeled GMP to the 5? end of targeted RNA species in a sample by optionally decapping followed by incubating the sample with an affinity tag-labeled GTP and a capping enzyme, enriching for RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag, reverse transcribing the enriched RNA to produce a population of cDNAs, and adding a tail to the 3? end of the population of cDNAs using a terminal transferase, to produce an cDNA library.Type: GrantFiled: October 17, 2017Date of Patent: January 18, 2022Assignee: New England Biolabs, Inc.Inventors: Bo Yan, Laurence Ettwiller, Ira Schildkraut, George Tzertzinis, Ivan R. Correa, Jr., Nan Dai, Madalee G. Wulf
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Publication number: 20210388433Abstract: A method for identifying any of the presence, 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/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase 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 with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.Type: ApplicationFiled: August 17, 2021Publication date: December 16, 2021Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Patent number: 11124825Abstract: A method for identifying any of the presence, 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/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase 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 with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.Type: GrantFiled: December 12, 2018Date of Patent: September 21, 2021Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Publication number: 20210207200Abstract: 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. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: ApplicationFiled: February 22, 2021Publication date: July 8, 2021Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Patent number: 11001876Abstract: 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. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: GrantFiled: February 27, 2019Date of Patent: May 11, 2021Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Publication number: 20200325533Abstract: Providing herein, among other things, is a method comprising incubating a double-stranded nucleic acid having a nick with a nick translating activity, a ligase, and a nucleotide mix comprising at least one modified nucleotide, to generate a product comprising a patch of a newly synthesized strand of a duplex nucleic acid containing a plurality of modified nucleoside monophosphates that are at or adjacent to the site of the nick. In some embodiments, the method may be used to map damaged nucleoside monophosphates in a nucleic acid. Compositions and kits for use in performing the method are also provided.Type: ApplicationFiled: August 21, 2018Publication date: October 15, 2020Applicant: New England Biolabs, Inc.Inventors: Kelly M. Zatopek, Vladimir Potapov, Jennifer Ong, Laurence Ettwiller, Lixin Chen, Thomas C. Evans, Jr., Andrew F. Gardner
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Patent number: 10619200Abstract: 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: GrantFiled: October 28, 2016Date of Patent: April 14, 2020Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Patent number: 10428368Abstract: 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: GrantFiled: April 25, 2016Date of Patent: October 1, 2019Assignee: New England Biolabs, Inc.Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, Jr., Michael Sproviero
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Publication number: 20190185919Abstract: 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: ApplicationFiled: February 27, 2019Publication date: June 20, 2019Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Patent number: 10260088Abstract: 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. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: GrantFiled: February 9, 2018Date of Patent: April 16, 2019Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Publication number: 20190100796Abstract: A method for identifying any of the presence, 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/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase 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 with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.Type: ApplicationFiled: December 12, 2018Publication date: April 4, 2019Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Patent number: 10227646Abstract: A method for identifying any of the presence, 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/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase 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 with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.Type: GrantFiled: February 24, 2017Date of Patent: March 12, 2019Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Publication number: 20180312914Abstract: 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: ApplicationFiled: October 28, 2016Publication date: November 1, 2018Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Publication number: 20180195061Abstract: A method of labeling, and optionally enriching, for a population of target RNA molecules in a mixture of RNAs is provided. In some embodiments, the method may comprise (a) adding a label to the 5? end of 5?-diphosphorylated or 5?-triphosphorylated target RNA molecules in a sample by incubating the sample with labeled GTP and a capping enzyme; and (b) optionally enriching for target RNA comprising the affinity tag-labeled GMP using an affinity matrix that binds to the affinity tag. The label may be an oligonucleotide, which may further comprise an affinity group attached either internally or at 5? or 3? end of the oligonucleotide where the oligonucleotide label may be added directly, or indirectly via a reaction with a reactive group to the target RNA.Type: ApplicationFiled: February 28, 2018Publication date: July 12, 2018Applicant: New England Biolabs, Inc.Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, Jr., George Tzertzinis, John Buswell, Madalee G. Wulf
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Publication number: 20180171397Abstract: 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. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: ApplicationFiled: February 9, 2018Publication date: June 21, 2018Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh