Patents by Inventor Ivan R. Correa, JR.
Ivan R. Correa, 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: 20230287489Abstract: The present disclosure relates, according to some embodiments, to compositions and analysis of RNA (e.g., dephosphorylated oligoribonucleotides) including, for example, natural and/or synthetic RNAs. A composition may comprise, for example, an endoribonuclease having an amino acid sequence that (i) corresponds to an amino acid sequence of a first species (e.g., Homo sapiens, Escherichia coli, Aspergillus oryzae, Momordica charantia, Pyrococcus furiosus, Cucumis sativus, and Sus scrofa) or (ii) is a non-naturally occurring sequence; and/or an RNA end repair enzyme having an amino acid sequence that (i) corresponds to an amino acid sequence of a species other than the first species (e.g., a bacterial species or a bacteriophage species) or (ii) is a non-naturally occurring sequence.Type: ApplicationFiled: April 10, 2023Publication date: September 14, 2023Applicant: New England Biolabs, Inc.Inventors: Ivan R. Correa, Jr., Eric Wolf, Nan Dai, Erbay Yigit, Sebastian Grünberg
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Publication number: 20230287376Abstract: The present disclosure relates, according to some embodiments, to immobilized enzyme compositions and methods for cleaving polynucleotide molecules including, for example, double-stranded DNA. Immobilized enzymes may comprise, for example, an enzyme (e.g., a type IIS restriction endonuclease, an RNAP, a capping enzyme), a support (e.g., a magnetic bead), and optionally, a linker disposed between the enzyme and the support. In some embodiments, methods may include contacting an immobilized enzyme with a polynucleotide substrate to form reaction products, separating the immobilized enzyme from the reaction products, and optionally reusing the immobilized enzymes in one or more subsequent reactions. preparing a library for sequencing.Type: ApplicationFiled: March 10, 2023Publication date: September 14, 2023Applicant: New England Biolabs, Inc.Inventors: Ming-Qun Xu, Guillermo García-Marquina, Siu-hong Chan, Ivan R. Correa, Jr., Aihua Zhang, Yi Fang, Michael Sproviero
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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: 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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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: 11525166Abstract: Kits 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 kits 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 kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.Type: GrantFiled: March 21, 2022Date of Patent: December 13, 2022Assignee: 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
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Patent number: 11512342Abstract: Provided herein is a composition comprising an enzyme that releases pyrophosphate from a substrate and a dye of Formula 1. A method for detecting pyrophosphate is also provided. A kit comprising a polymerase that releases pyrophosphate by hydrolysis of nucleoside triphosphates during nucleic acid replication, a divalent manganese salt, and the dye are also provided. The present composition, method and kits provide a way to detect and/or quantify substrates or products of enzyme reacted substrates associated with the release pyrophosphate (e.g., nucleic acid amplification reactions and other reactions that hydrolyze ATP) via a distinct color change without substantially affecting the sensitivity and/or specificity of the reaction.Type: GrantFiled: May 4, 2022Date of Patent: November 29, 2022Assignee: New England Biolabs, Inc.Inventors: Nathan Tanner, Ivan R. Correa, Jr., Yinhua Zhang, Ece Alpaslan
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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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Publication number: 20220213564Abstract: Kits 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 kits 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 kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.Type: ApplicationFiled: March 21, 2022Publication date: July 7, 2022Applicant: 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
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Publication number: 20220195424Abstract: Provided herein is a method for chemically capping polynucleotides having a 5? monophosphate. In some embodiments the method may comprise: combining an activated nucleoside 5? mono- or poly-phosphate with a population of polynucleotides that comprises polynucleotides having a 5? monophosphate, to produce a reaction mix; and incubating the reaction mix to produce reaction products that comprise a polynucleotide and a 5? nucleoside cap, linked by a 5? to 5? polyphosphate linkage. The chemical capping method described herein can be incorporated into a variety of cDNA synthesis methods.Type: ApplicationFiled: May 6, 2020Publication date: June 23, 2022Applicant: New England Biolabs, Inc.Inventors: Ivan R. Correa, Jr., Shengxi Guan, Madalee G. Wulf, Nan Dai, Sean Maguire
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Patent number: 11345970Abstract: Kits 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 kits 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 kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.Type: GrantFiled: August 19, 2021Date of Patent: May 31, 2022Assignee: 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
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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: 20210404024Abstract: Kits 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 kits 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 kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.Type: ApplicationFiled: August 19, 2021Publication date: December 30, 2021Applicant: 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, D.Phil., Ivan R. Correa, Jr., Clotilde Carlow, Esta Slayton
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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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Patent number: 10081827Abstract: Methods, compositions and kits for selectively altering and detecting modified cytosine residues are provided.Type: GrantFiled: January 12, 2016Date of Patent: September 25, 2018Assignee: New England Biolabs, Inc.Inventors: Shengxi Guan, Nan Dai, Zhenyu Zhu, Ivan R. Correa, Jr., Aine Quimby, Janine Borgaro
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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: 20180030436Abstract: 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: ApplicationFiled: October 17, 2017Publication date: February 1, 2018Applicant: 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: 20170253911Abstract: 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: ApplicationFiled: April 25, 2016Publication date: September 7, 2017Applicant: New England Biolabs, Inc.Inventors: Ira Schildkraut, Laurence Ettwiller, Ivan R. Correa, Jr., Michael Sproviero
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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