Patents by Inventor Thomas C. Evans, Jr.
Thomas C. Evans, Jr. 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: 20230407419Abstract: Compositions and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The compositions and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The compositions and methods are directed to labelled probes and their uses in Loop-Mediated Isothermal Amplification (LAMP) diagnostic tests to detect target DNA from the environment or from an individual and also to detect specific variants of the target DNA, both with similar sensitivity.Type: ApplicationFiled: August 18, 2023Publication date: December 21, 2023Applicant: New England Biolabs, Inc.Inventors: Nathan Tanner, Yinhua Zhang, Eric Hunt, Gregory Patton, Guoping Ren, Zhiru Li, Andrew Barry, Nicole Nichols, Catherine B. Poole, Harriet M. Strimpel, Ivan R. Correa, Jr., Clotilde Carlow, Esta Slayton, Thomas C. Evans, Jr.
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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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Patent number: 11732315Abstract: Compositions and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The compositions and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The compositions and methods are directed to labelled probes and their uses in Loop-Mediated Isothermal Amplification (LAMP) diagnostic tests to detect target DNA from the environment or from an individual and also to detect specific variants of the target DNA, both with similar sensitivity.Type: GrantFiled: September 28, 2022Date of Patent: August 22, 2023Assignee: New England Biolabs, Inc.Inventors: Nathan Tanner, Yinhua Zhang, Eric Hunt, Gregory Patton, Guoping Ren, Zhiru Li, Andrew Barry, Nicole Nichols, Catherine B. Poole, Harriet M. Strimpel, Ivan R. Correa, Jr., Clotilde Carlow, Esta Slayton, Thomas C. Evans, Jr.
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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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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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Patent number: 11639498Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.Type: GrantFiled: August 20, 2018Date of Patent: May 2, 2023Assignee: New England Biolabs, Inc.Inventors: Pei-Chung Hsieh, Luo Sun, Thomas C. Evans, Jr., Theodore B. Davis, Andrew F. Gardner
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Publication number: 20230048863Abstract: Compositions and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The compositions and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The compositions and methods are directed to labelled probes and their uses in Loop-Mediated Isothermal Amplification (LAMP) diagnostic tests to detect target DNA from the environment or from an individual and also to detect specific variants of the target DNA, both with similar sensitivity.Type: ApplicationFiled: September 28, 2022Publication date: February 16, 2023Applicant: New England Biolabs, Inc.Inventors: Nathan Tanner, Yinhua Zhang, Eric Hunt, Gregory Patton, Guoping Ren, Zhiru Li, Andrew Barry, Nicole Nichols, Catherine B. Poole, Harriet M. Strimpel, Ivan R. Correa, JR., Clotilde Carlow, Esta Slayton, Thomas C. Evans, JR.
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Patent number: 11162133Abstract: Methods are provided for a rapid, low cost approach to monitoring an amplification reaction. This includes monitoring the progress of isothermal or PCR amplification reactions to completion using pH-sensitive dyes that are either colored or fluorescent. Compositions are described that include a mixture of a DNA polymerase, deoxyribonucleotide triphosphate and Tris buffer in the range of 1.5 mM Tris to 5 mM Tris or equivalent.Type: GrantFiled: May 12, 2017Date of Patent: November 2, 2021Assignee: New England Biolabs, Inc.Inventors: Yinhua Zhang, Nathan Tanner, Thomas C. Evans, Jr.
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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: 10597710Abstract: 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: GrantFiled: August 28, 2015Date of Patent: March 24, 2020Assignee: New England Biolabs, Inc.Inventors: Gregory Lohman, Thomas C. Evans, Jr., Larry A. McReynolds
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Publication number: 20190169683Abstract: Methods are provided for a rapid, low cost approach to monitoring an amplification reaction. This includes monitoring the progress of isothermal or PCR amplification reactions to completion using pH-sensitive dyes that are either colored or fluorescent. Compositions are described that include a mixture of a DNA polymerase, deoxyribonucleotide triphosphate and Tris buffer in the range of 1.5 mM Tris to 5 mM Tris or equivalent.Type: ApplicationFiled: May 12, 2017Publication date: June 6, 2019Applicant: New England Biolabs, Inc.Inventors: Yinhua Zhang, Nathan Tanner, Thomas C. Evans, Jr.
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Patent number: 10301673Abstract: Provided herein is a method for reducing amplification of non-template molecules in a nucleic acid sample. In certain embodiments, the method involves adding a helicase to a reaction mixture for non-helicase-dependent amplification of target nucleic acid.Type: GrantFiled: February 5, 2018Date of Patent: May 28, 2019Inventors: Nathan Tanner, Thomas C. Evans, Jr.
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Patent number: 10246706Abstract: Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3? end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.Type: GrantFiled: April 9, 2018Date of Patent: April 2, 2019Assignee: New England Biolabs, Inc.Inventors: Shengxi Guan, Thomas C. Evans, Jr., Nicole Nichols, Yanxia Bei
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Patent number: 10240148Abstract: Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3? end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.Type: GrantFiled: August 18, 2016Date of Patent: March 26, 2019Assignee: New England Biolabs, Inc.Inventors: Shengxi Guan, Thomas C. Evans, Jr., Nicole Nichols, Yanxia Bei
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Publication number: 20180355328Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.Type: ApplicationFiled: August 20, 2018Publication date: December 13, 2018Applicant: New England Biolabs, Inc.Inventors: Pei-Chung Hsieh, Luo Sun, Thomas C. Evans, JR., Theodore B. Davis, Andrew F. Gardner
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Patent number: 10081799Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.Type: GrantFiled: February 14, 2017Date of Patent: September 25, 2018Assignee: New England Biolabs, Inc.Inventors: Pei-Chung Hsieh, Luo Sun, Thomas C. Evans, Jr., Theodore B. Davis, Andrew Gardner
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Publication number: 20180223276Abstract: Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3? end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.Type: ApplicationFiled: April 9, 2018Publication date: August 9, 2018Applicant: New England Biolabs, Inc.Inventors: Shengxi Guan, Thomas C. Evans, JR., Nicole Nichols, Yanxia Bei
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Patent number: 10041051Abstract: This disclosure provides, among other things, a composition comprising: comprising a fusion protein comprising: (a) a DNA polymerase; and (b) a heterologous sequence-specific DNA binding domain. A method for copying a DNA template, as well as a kit for performing the same, are also described.Type: GrantFiled: February 14, 2017Date of Patent: August 7, 2018Assignee: New England Biolabs, Inc.Inventors: Pei-Chung Hsieh, Luo Sun, Thomas C. Evans, Jr., Theodore B. Davis, Andrew Gardner
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Publication number: 20180216098Abstract: This disclosure provides, among other things, a composition comprising: a 5? exonuclease; a strand-displacing polymerase; and optionally a single strand DNA binding protein and/or a ligase. A method for polynucleotide assembly to form a synthon, as well as a kit for performing the same, are also described.Type: ApplicationFiled: August 27, 2015Publication date: August 2, 2018Applicant: New England Biolabs, Inc.Inventors: Pei-Chung Hsieh, Luo Sun, Thomas C. Evans, Jr., Theodore B. Davis, Andrew Gardner
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Publication number: 20180171399Abstract: Provided herein is a method for reducing amplification of non-template molecules in a nucleic acid sample. In certain embodiments, the method involves adding a helicase to a reaction mixture for non-helicase-dependent amplification of target nucleic acid.Type: ApplicationFiled: February 5, 2018Publication date: June 21, 2018Applicant: New England Biolabs, Inc.Inventors: Nathan Tanner, Thomas C. Evans, JR.