Patents by Inventor Romualdas Vaisvila
Romualdas Vaisvila 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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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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Publication number: 20230357838Abstract: Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 21, 40, 47, 49, 50, 55, 58, 59, 62, 63, 65, 67, 70, 71, 76, 106, 107, 110, 112, 114, 117, 163 and/or 164 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.Type: ApplicationFiled: May 24, 2023Publication date: November 9, 2023Applicant: New England Biolabs, Inc.Inventors: Zhiyi Sun, Sean R. Johnson, Bo Yan, Lixin Chen, G. Brett Robb, Thomas C. Evans, JR., Romualdas Vaisvila
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Publication number: 20230257730Abstract: Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 24, 26, 27, 28, 33, 40, 49, 50, 63, 95, 96, 97, and/or 99 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.Type: ApplicationFiled: November 22, 2022Publication date: August 17, 2023Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Sean R. Johnson, Zhiyi Sun, Thomas C. Evans, JR.
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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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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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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: 20180362960Abstract: Among other things, a method for performing multiple enzyme reactions in a single tube is provided. In some embodiments, the method may comprise producing a reaction mix comprising a thermolabile UDG, an AP lyase and DNA fragments that comprise one or more uracil residues, incubating the reaction mix at a relatively low temperature to cleave fragments at the one or more uracil residues, raising the temperature of the reaction mix to a relatively high temperature to inactivate the thermolabile UDG; and deaminating the fragments, thereby converting any cytosine in the fragments of DNA to uracil.Type: ApplicationFiled: June 15, 2017Publication date: December 20, 2018Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Lauren Higgins, Ashley Luck
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Patent number: 10155939Abstract: Among other things, a method for performing multiple enzyme reactions in a single tube is provided. In some embodiments, the method may comprise producing a reaction mix comprising a thermolabile UDG, an AP lyase and DNA fragments that comprise one or more uracil residues, incubating the reaction mix at a relatively low temperature to cleave fragments at the one or more uracil residues, raising the temperature of the reaction mix to a relatively high temperature to inactivate the thermolabile UDG; and deaminating the fragments, thereby converting any cytosine in the fragments of DNA to uracil.Type: GrantFiled: June 15, 2017Date of Patent: December 18, 2018Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Lauren Higgins, Ashley Luck
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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: 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
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Patent number: 9896726Abstract: Compositions and methods are provided for discrimination between cytosine and modifications thereof using cytidine deaminases and/or oxygenases. Variants of wild type cytidine deaminases are described which show reduced bias with respect to adjacent nucleotides upstream of the cytosine. The methods provide a rapid and convenient use of enzymes to obtain methylomes.Type: GrantFiled: July 22, 2015Date of Patent: February 20, 2018Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Heidi E. Johnson, Saulius Vainauskas, Theodore B. Davis
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Publication number: 20170198344Abstract: 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: February 24, 2017Publication date: July 13, 2017Applicant: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Zhiyi Sun, Shengxi Guan, Lana Saleh, Laurence Ettwiller, Theodore B. Davis
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Patent number: 9464277Abstract: 5-methylpyrimidine oxygenases and their use in the modification of nucleic acids are described.Type: GrantFiled: April 20, 2015Date of Patent: October 11, 2016Assignee: New England Biolabs, Inc.Inventors: Yu Zheng, Lana Saleh, June Pais, Nan Dai, Richard J. Roberts, Ivan R. Correa, Jr., Megumu Mabuchi, Romualdas Vaisvila
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Publication number: 20150322506Abstract: Compositions and methods are provided for discrimination between cytosine and modifications thereof using cytidine deaminases and/or oxygenases. Variants of wild type cytidine deaminases are described which show reduced bias with respect to adjacent nucleotides upstream of the cytosine. The methods provide a rapid and convenient use of enzymes to obtain methylomes.Type: ApplicationFiled: July 22, 2015Publication date: November 12, 2015Applicant: NEW ENGLAND BIOLABS, INC.Inventors: Romualdas Vaisvila, Heidi E. Johnson, Saulius Vainauskas, Theodore B. Davis