Patents by Inventor Vladimir Potapov
Vladimir Potapov 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: 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: 20220380741Abstract: The present disclosure relates, according to some embodiments, to systems, apparatus, compositions, methods, and workflows that include DNase I variants with desirable properties including, for example, salt tolerance. A DNase I variant, in some embodiments, may have an amino acid sequence that is at least 85% identical, at least 90% identical, at least 95% identical, and/or at least 98% identical to SEQ ID NO:1 and may be identical to SEQ ID NO:1 at one or more positions selected from the group of positions corresponding to L29, A35, D87, Q88, S94, P103, T108, P121, P132, A135, D145, E161, G172, P190, H208, and A224 of SEQ ID NO:1.Type: ApplicationFiled: May 27, 2021Publication date: December 1, 2022Applicant: New England Biolabs, Inc.Inventors: Heidi Crosby, Jennifer Ong, Ashley Luck, Eric J. Cantor, Vladimir Potapov
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Publication number: 20220380738Abstract: The present disclosure relates, according to some embodiments, to compositions, methods, systems, and kits for programmable endonucleolytic cleavage of DNA (e.g., ds DNA). For example, the in vitro activity of an Argonaute (e.g., a mesophilic Argonaute CbAgo from Clostridium butyricum) may be synchronized with DNA strand unwinding activity of a helicase (e.g., a nuclease deficient RecBexo-C DNA helicase from E. coli) for a rapid and efficient cleavage of double-stranded DNA targets. Enzymatic properties of CbAgo and different aspects of ds DNA cleavage were thoroughly explored by adapting high-throughput capillary electrophoreses technique for monitoring CbAgo cleavage activity in concurrence with RecBexo-C. The present disclosure shows that in the presence of RecBexo-C, CbAgo can be programmed with guides to cleave any site of interest localized at up to 10 kb distance from the end of linear ds DNA at 37° C. temperature.Type: ApplicationFiled: June 1, 2021Publication date: December 1, 2022Applicant: New England Biolabs, Inc.Inventors: Jurate Bitinaite, Rita Vaiskunaite, Vladimir Potapov, Nathan Tanner
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Publication number: 20220275352Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: ApplicationFiled: May 11, 2022Publication date: September 1, 2022Applicant: New England Biolabs, Inc.Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
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Patent number: 11371028Abstract: Variants of the bacteriophage B103 DNA polymerase are described herein. The variant has improved properties, that include when compared to wild-type Phi29 DNA polymerase, at least one of the following: increased thermostability, improved reaction rate for DNA amplification, reduced background and a reduction of bias. Methods of using the DNA polymerase variant are also described herein.Type: GrantFiled: January 25, 2021Date of Patent: June 28, 2022Assignee: New England Biolabs, Inc.Inventors: Jennifer Ong, Nathan Tanner, Yinhua Zhang, Yanxia Bei, Vladimir Potapov
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Patent number: 11359184Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: GrantFiled: November 11, 2019Date of Patent: June 14, 2022Assignee: New England Biolabs, Inc.Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
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Publication number: 20220177875Abstract: Ordered assembly of large numbers of fragments into a single large DNA have been improved in both frequency and fidelity of the assembled product. This has been achieved by novel compositions and methods that are utilized in a computer system that integrates comprehensive ligation data from multiple sources to provide optimized synthetic overhangs or overhangs from restriction endonuclease cleavage on DNA fragments for assembly by ligation. Intragenic cut sites are avoided by the use of a novel restriction endonuclease which recognizes 7 nucleotides (bases) and cuts DNA to create 4-base overhangs with the help of a synthetic activator oligonucleotide. Variations in ligation preferences by different ligases provide extra precision in assembly reactions. The use of the improved methods are exemplified by the successful assembly from 52 fragments of a viral genome and also a 52 fragment ordered assembly of a bacteria operon.Type: ApplicationFiled: December 17, 2021Publication date: June 9, 2022Applicant: New England Biolabs, Inc.Inventors: Gregory Lohman, Vladimir Potapov, John M. Pryor, Rebecca Kucera, Katharina Bilotti, Richard D. Morgan
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Publication number: 20220098577Abstract: A composition and its uses and additionally a kit are provided. The composition is a synthetic self-complementary oligonucleotide that has a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl. Additionally, the oligonucleotide includes unligatable 3? and 5? ends that cannot be cleaved by PaqCl. This oligonucleotide composition has been combined with PaqCl or a variant of PaqCl Type IIS restriction endonuclease in a reaction mixture, where the reaction mixture includes PaqCl or variant that can further be combined with a ligase and optionally a deadenylase, crowding molecule such as PEG and/or a repair enzyme such as Endo MS. The kit includes the oligonucleotide and Type IIS restriction endonuclease in the same or different containers.Type: ApplicationFiled: December 15, 2021Publication date: March 31, 2022Applicant: New England Biolabs, Inc.Inventors: Gregory Lohman, John M. Pryor, Rebecca Kucera, Vladimir Potapov, Katharina Bilotti, Richard D. Morgan
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Publication number: 20210383891Abstract: Methods and compositions are provided for optimizing ordered assembly of a plurality of polynucleotide fragments. The optimization involves providing sets of overhang sequences with preferred experimental conditions for high fidelity ordered assembly of polynucleotide fragments by ligation under selected experimental conditions. The methods and compositions provide the use of a computer system with inputs having a plurality of menus and outputs that include a variety of media interfaces. The computer system has access to a ligation frequency database to provide sets of overhang sequences for efficient joining of multiple fragments into the target nucleic acid.Type: ApplicationFiled: October 17, 2019Publication date: December 9, 2021Applicant: New England Biolabs, Inc.Inventors: Gregory Lohman, Vladimir Potapov, John M. Pryor, Rebecca Kucera
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Publication number: 20210155909Abstract: Variants of the bacteriophage B103 DNA polymerase are described herein. The variant has improved properties, that include when compared to wild-type Phi29 DNA polymerase, at least one of the following: increased thermostability, improved reaction rate for DNA amplification, reduced background and a reduction of bias. Methods of using the DNA polymerase variant are also described herein.Type: ApplicationFiled: January 25, 2021Publication date: May 27, 2021Applicant: New England Biolabs, Inc.Inventors: Jennifer Ong, Nathan Tanner, Yinhua Zhang, Yanxia Bei, Vladimir Potapov
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Patent number: 10934533Abstract: Variants of the bacteriophage B103 DNA polymerase are described herein. The variant has improved properties, that include when compared to wild-type Phi29 DNA polymerase, at least one of the following: increased thermostability, improved reaction rate for DNA amplification, reduced background and a reduction of bias. Methods of using the DNA polymerase variant are also described herein.Type: GrantFiled: October 10, 2019Date of Patent: March 2, 2021Assignee: New England Biolabs, Inc.Inventors: Jennifer Ong, Nathan Tanner, Yinhua Zhang, Yanxia Bei, Vladimir Potapov
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Patent number: 10837009Abstract: Mutant bacteriophage DNA ligases that have increased tolerance to salt and/or heat is provided. Methods, compositions and kits that employ the same are also provided.Type: GrantFiled: December 20, 2018Date of Patent: November 17, 2020Assignee: New England Biolabs, Inc.Inventors: Jennifer Ong, Gregory Lohman, Aine Quimby, Vladimir Potapov, John M. Pryor
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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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Publication number: 20200123513Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: ApplicationFiled: November 11, 2019Publication date: April 23, 2020Applicant: New England Biolabs, Inc.Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
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Patent number: 10519431Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: GrantFiled: May 12, 2017Date of Patent: December 31, 2019Assignee: New England Biolabs, Inc.Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
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Publication number: 20190024061Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: ApplicationFiled: January 12, 2017Publication date: January 24, 2019Applicant: New England Biolabs, Inc.Inventors: Jennifer Ong, Shaorong Chong, Haruichi Asahara, Kuo-Chan Hung, Vladimir Potapov, George Tzertzinis
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Publication number: 20170247670Abstract: A bacteriophage RNA polymerase variant is provided. In some embodiments, the variant may have increased thermostability relative to the corresponding wild type bacteriophage RNA polymerase and/or wild type T7 RNA polymerase. Compositions, kits and methods that employ the variant are also provided.Type: ApplicationFiled: May 12, 2017Publication date: August 31, 2017Applicant: New England Biolabs, Inc.Inventors: Jennifer Ong, Vladimir Potapov, Kuo-Chan Hung, Haruichi Asahara, Shaorong Chong, George Tzertzinis
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Patent number: 8416864Abstract: A method and modem are provided for obtaining an optimized efficiency of an Orthogonal Frequency Division Multiplex (OFDM) data transmission, such as for power line communication, for example. The length or duration of a guard interval or cyclic prefix in an OFDM symbol is newly selected at each start-up of a modem while initializing or preparing the OFDM data transmission. The length of the guard interval can be given by the number of samples in a time-discrete representation, and the value of such number of samples that is retained for the subsequent data transmission can be selected from a plurality of pre-determined possibilities based on an evaluation of a channel quality of a communication channel including a physical line to which the modem is connected. Hence, the selected value depends on actual transmission conditions, and the optimization potential offered by a more flexible handling of system parameters is exploited to meet changing conditions on the physical line.Type: GrantFiled: June 29, 2009Date of Patent: April 9, 2013Inventors: Dmitri Korobkov, Patrick Langfeld, Vladimir Potapov, Christian Leeb, Hans-Joerg Maag, Hans Benninger, Stefan Ramseier
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Publication number: 20100054314Abstract: A method and modem are provided for obtaining an optimized efficiency of an Orthogonal Frequency Division Multiplex (OFDM) data transmission, such as for power line communication, for example. The length or duration of a guard interval or cyclic prefix in an OFDM symbol is newly selected at each start-up of a modem while initializing or preparing the OFDM data transmission. The length of the guard interval can be given by the number of samples in a time-discrete representation, and the value of such number of samples that is retained for the subsequent data transmission can be selected from a plurality of pre-determined possibilities based on an evaluation of a channel quality of a communication channel including a physical line to which the modem is connected. Hence, the selected value depends on actual transmission conditions, and the optimization potential offered by a more flexible handling of system parameters is exploited to meet changing conditions on the physical line.Type: ApplicationFiled: June 29, 2009Publication date: March 4, 2010Applicant: ABB TECHNOLOGY AGInventors: Dmitri Korobkov, Patrick Langfeld, Vladimir Potapov, Christian Leeb, Hans-Joerg Maag, Hans Benninger, Stefan Ramseier