Patents by Inventor Theo Nikiforov
Theo Nikiforov 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: 20240132955Abstract: Provided herein are reagents, compositions, and methods for sequencing nucleic acids. Among the reagents disclosed are nucleotides labeled with cleavable linkers. Certain linkers are configured to undergo immolation reactions following cleavage, which can generate scars with enhanced properties for nucleic acid sequencing and synthesis. The present disclosure also provides reagents, compositions, and methods for capping scars generated through linker cleavage, which can alter scar properties, and in some cases can increase the rate and accuracy of nucleotide incorporations during polymerization.Type: ApplicationFiled: September 27, 2023Publication date: April 25, 2024Inventors: Linda LEE, Theo Nikiforov, Alexander Joseph Limardo, Maya H. Reamey, Steven Menchen, Gilad Almogy
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Publication number: 20240067941Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.Type: ApplicationFiled: October 13, 2023Publication date: February 29, 2024Inventors: Peter VANDER HORN, Theo NIKIFOROV, Daniel MAZUR, Eileen TOZER, Mindy LANDES
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Patent number: 11821011Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.Type: GrantFiled: August 13, 2021Date of Patent: November 21, 2023Assignee: Life Technologies CorporationInventors: Peter Vander Horn, Daniel Mazur, Theo Nikiforov, Mindy Landes, Eileen Tozer
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Publication number: 20230340570Abstract: The present disclosure provides methods, systems, compositions, and kits for reducing particle aggregation and improving sequencing quality. A method for processing particles may comprise the use of a first buffer solution or a second buffer solution. A method for processing particles may comprise the use of a single-strand binding moiety such as a single-strand binding protein.Type: ApplicationFiled: February 24, 2023Publication date: October 26, 2023Inventors: Daniel MAZUR, Kevin HEINEMANN, Theo NIKIFOROV, Robert ONO, Aklilu WORKU, Florian OBERSTRASS
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Publication number: 20230332226Abstract: The present disclosure provides compositions, methods, and systems for enrichment and analysis of template nucleic acid molecules, e.g., of a biological sample. Further provided herein are methods of using a plurality of unique bead species each comprising a unique set of identical primer molecules.Type: ApplicationFiled: February 28, 2023Publication date: October 19, 2023Inventors: Florian OBERSTRASS, Theo NIKIFOROV, Mark STAPLETON, Daniel MAZUR, Gilad ALMOGY, Ishminder MANN, Chandan SHEE, Benjamin SCHROEDER
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Publication number: 20230193223Abstract: Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.Type: ApplicationFiled: September 16, 2022Publication date: June 22, 2023Inventors: Peter VANDER HORN, Cheng-Yao CHEN, Guobin LUO, Michael PREVITE, Jamshid TEMIROV, Theo NIKIFOROV, Zhaohui ZHOU, Hongye SUN, Yufang WANG, Stefanie Yukiko NISHIMURA, Hongyi WANG, Marian PERIS, Barnett ROSENBLUM, Michael PHELAN
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Publication number: 20230183778Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.Type: ApplicationFiled: November 11, 2022Publication date: June 15, 2023Inventors: Eliane TREPAGNIER, Mark PRATT, Theo NIKIFOROV, Gilad ALMOGY
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Patent number: 11542549Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are labeled polymerase conjugates including a polymerase linked to one or more labels, wherein the conjugate has polymerase activity. Such conjugates can exhibit enhanced biological activity and/or superior detectability as compared to conventional labeled polymerases. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.Type: GrantFiled: February 28, 2018Date of Patent: January 3, 2023Assignee: LIFE TECHNOLOGIES CORPORATIONInventor: Theo Nikiforov
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Patent number: 11505820Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.Type: GrantFiled: July 23, 2020Date of Patent: November 22, 2022Assignee: ULTIMA GENOMICS, INC.Inventors: Eliane Trepagnier, Mark Pratt, Theo Nikiforov, Gilad Almogy
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Publication number: 20220348994Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.Type: ApplicationFiled: April 4, 2022Publication date: November 3, 2022Inventors: Linda LEE, Steven MENCHEN, Theo NIKIFOROV, Gilad ALMOGY, Florian OBERSTRASS
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Patent number: 11447756Abstract: Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.Type: GrantFiled: March 20, 2020Date of Patent: September 20, 2022Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Peter Vander Horn, Cheng-Yao Chen, Guobin Luo, Michael Previte, Jamshid Temirov, Theo Nikiforov, Zhaohui Zhou, Hongye Sun, Yufang Wang, Stefanie Yukiko Nishimura, Hongyi Wang, Marian Peris, Barnett Rosenblum, Michael Phelan
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Publication number: 20220162573Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragment thereof are provided that allow for nucleic acid amplification. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates for use in various downstream processes. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered catalytic properties. In some aspects, the disclosure provides modified polymerases having enhanced catalytic properties as compared to a reference polymerase.Type: ApplicationFiled: December 20, 2021Publication date: May 26, 2022Inventors: Peter VANDER HORN, Theo NIKIFOROV, Guobin LUO, Mindy LANDES, Daniel MAZUR, Eileen TOZER, Tommie LINCECUM
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Publication number: 20220162660Abstract: In some embodiments, the disclosure relates generally to methods, as well as related compositions and kits for recombinase-mediated nucleic acid amplification, such as recombinase-polymerase amplification (RPA), of a nucleic acid template using at least one blocked primer that contains a 5? domain, at least one nucleotide that is cleavable by an RNase H enzyme, a 3? domain, wherein the primer is not extendable by a polymerase, and wherein the 3? domain has a length of 7-100 nucleotides, for example 10-30 nucleotides. These methods and the use of a blocked primer reduce or eliminate non-specific amplification products, such as primer dimers, which are generated in RPA reactions.Type: ApplicationFiled: February 8, 2022Publication date: May 26, 2022Inventors: Hua YU, Theo NIKIFOROV, Abraham ROSENBAUM
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Patent number: 11326203Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.Type: GrantFiled: March 18, 2020Date of Patent: May 10, 2022Assignee: Ultima Genomics, Inc.Inventors: Linda Lee, Steven Menchen, Theo Nikiforov, Gilad Almogy, Florian Oberstrass
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Patent number: 11268117Abstract: In some embodiments, the disclosure relates generally to methods, as well as related compositions and kits for recombinase-mediated nucleic acid amplification, such as recombinase-polymerase amplification (RPA), of a nucleic acid template using at least one blocked primer that contains a 5? domain, at least one nucleotide that is cleavable by an RNase H enzyme, a 3? domain, wherein the primer is not extendable by a polymerase, and wherein the 3? domain has a length of 7-100 nucleotides, for example 10-30 nucleotides. These methods and the use of a blocked primer reduce or eliminate non-specific amplification products, such as primer dimers, which are generated in RPA reactions.Type: GrantFiled: June 9, 2017Date of Patent: March 8, 2022Assignee: Life Technologies CorporationInventors: Hua Yu, Theo Nikiforov, Abraham Rosenbaum
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Patent number: 11208636Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragment thereof are provided that allow for nucleic acid amplification. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates for use in various downstream processes. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered catalytic properties. In some aspects, the disclosure provides modified polymerases having enhanced catalytic properties as compared to a reference polymerase.Type: GrantFiled: April 16, 2020Date of Patent: December 28, 2021Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Peter Vander Horn, Theo Nikiforov, Guobin Luo, Mindy Landes, Daniel Mazur, Eileen Tozer, Tommie Lincecum
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Publication number: 20210371834Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.Type: ApplicationFiled: August 13, 2021Publication date: December 2, 2021Inventors: Peter VANDER HORN, Daniel MAZUR, Theo NIKIFOROV, Mindy LANDES, Eileen TOZER
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Patent number: 11091746Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.Type: GrantFiled: June 5, 2020Date of Patent: August 17, 2021Assignee: Life Technologies CorporationInventors: Peter Vander Horn, Daniel Mazur, Theo Nikiforov, Mindy Landes, Eileen Tozer
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Patent number: 11047004Abstract: The present disclosure provide systems, compositions, methods, reagents, kits and products for extending a nucleic acid that includes incorporating a nucleotide residue at a terminus of a nucleic acid using a polymerase enzyme and at least one nucleotide, wherein the at least one nucleotide includes a thiophosphate moiety, and wherein the at least one nucleotide is resistant to hydrolysis by phosphatase. In some embodiments, the nucleotide incorporation can be conducted in the presence of a phosphatase. In some embodiments, the nucleotide incorporation can be conducted in the presence of at least on chelation moiety that is configured to bind an orthophosphate moiety.Type: GrantFiled: May 23, 2019Date of Patent: June 29, 2021Assignee: Life Technologies CorporationInventors: Steven Menchen, Theo Nikiforov, Barnett Rosenblum
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Patent number: 11015220Abstract: Disclosed herein are conjugates comprising a biomolecule linked to a label that have biological activity and are useful in a wide variety of biological applications. For example, provided herein are polymerase-nanoparticle conjugates including a polymerase linked to a nanoparticle, wherein the conjugate has polymerase activity. Such conjugates can exhibit reduced aggregation and improved stochiometries wherein the average biomolecule:nanoparticle ratio approaches or equals 1:1. Also disclosed herein are improved methods for preparing such conjugates, and methods and systems for using such conjugates in biological applications such as nucleotide incorporation, primer extension and single molecule sequencing.Type: GrantFiled: September 6, 2018Date of Patent: May 25, 2021Assignee: Life Technologies CorporationInventors: Theo Nikiforov, Daniel Mazur, Xinzhan Peng, Tommie Lloyd Lincecum, Yuri Belosludtsev, Howard Reese, Dmitriy Gremyachinskiy, Roman Rozhkov, John Mauro, Joseph Beechem, Eric Tulsky, Imad Naasani, Kari Haley, Joseph Treadway