Patents by Inventor Aruna AYER
Aruna AYER 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: 10851353Abstract: The present disclosure provides variant Pol6 polymerase polypeptides, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.Type: GrantFiled: March 19, 2019Date of Patent: December 1, 2020Assignees: Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc.Inventors: Evan Amato, Cleoma Arnold, Aruna Ayer, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin McGaw, Preethi Sarvabhowman, Charles Wayan Schwab, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Wunderlich
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Patent number: 10829747Abstract: The present disclosure provides variant Pol6 polymerase polypeptides, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.Type: GrantFiled: September 20, 2017Date of Patent: November 10, 2020Assignees: Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc.Inventors: Aruna Ayer, Cleoma Arnold, Charles Schwab, Preethi Sarvabhowman, Eileen Thai, Ilya Lederman, Colin McGaw, Evan Amato, Barbara Eckert, Shawn Suko, Mara Boenitz-Dulat, Bigna Woersdoerfer, David Wunderlich
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Publication number: 20200283842Abstract: The present disclosure is directed to compositions and methods for deriving a plurality of kinetics parameters (240) for at least two different enzyme variants in a multiplex manner using nanopore-based sequencing. In some embodiments, the systems and methods may be used to screen different nanopore variants, or different combinations of both nanopore variants and enzyme variants.Type: ApplicationFiled: February 21, 2020Publication date: September 10, 2020Inventors: Aruna AYER, George M. CHURCH, Mirko PALLA, Francios PEPIN, Sukanya Srinivasa Rao Arun PUNTHAMBAKER, Peter B. STRANGES
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Publication number: 20200277581Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: ApplicationFiled: May 11, 2020Publication date: September 3, 2020Applicant: Roche Sequencing Solutions, Inc.Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS
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Publication number: 20200270589Abstract: Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.Type: ApplicationFiled: May 11, 2020Publication date: August 27, 2020Applicant: ROCHE SEQUENCING SOLUTIONS, INC.Inventors: Helen FRANKLIN, Cynthia CECH, Timothy Kellogg CRAIG, Aruna AYER, Kirti DHIMAN, Natalie B. CHECHELSKI JOHNSTON, Joshua N. MABRY, Arkadiusz BIBILLO, Peter CRISALLI, Randall W. DAVIS
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Publication number: 20200263248Abstract: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.Type: ApplicationFiled: March 18, 2020Publication date: August 20, 2020Applicant: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Meng Taing, Aruna Ayer, Peter J. Crisalli
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Publication number: 20200190572Abstract: The present disclosure provides variant Pol6 polymerase polypeptides, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.Type: ApplicationFiled: February 26, 2020Publication date: June 18, 2020Inventors: Aruna Ayer, Preethi Sarvabhowman, Dhruti Vasudev Dalal
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Publication number: 20200190489Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365Q, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: ApplicationFiled: February 26, 2020Publication date: June 18, 2020Inventors: Aruna Ayer, Cleoma Renetta Arnold, Arkadiusz Bibillo, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin Alexander McGaw, Charles Wayan Schwab, Tyler O'Brien Shultz, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Daniel Wunderlich
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Patent number: 10655174Abstract: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.Type: GrantFiled: May 24, 2017Date of Patent: May 19, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Dmitriy Gremyachinskiy, Meng Taing, Aruna Ayer, Peter J. Crisalli
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Patent number: 10612009Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365Q, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, 1644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: GrantFiled: April 29, 2019Date of Patent: April 7, 2020Assignees: Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc.Inventors: Aruna Ayer, Cleoma Renetta Arnold, Arkadiusz Bibillo, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin Alexander McGaw, Charles Wayan Schwab, Tyler O'Brien Shultz, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Daniel Wunderlich
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Publication number: 20200087636Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: ApplicationFiled: November 25, 2019Publication date: March 19, 2020Inventors: Aruna AYER, Cleoma ARNOLD, Charles Wayan SCHWAB, Eileen THAI, Ilya LEDERMAN, Colin Alexander MCGAW, Tyler O'Brien SHULTZ
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Patent number: 10590480Abstract: The present of disclosure provides variant Pol6 polymerase polypeptide, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.Type: GrantFiled: February 27, 2017Date of Patent: March 17, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Preethi Sarvabhowman, Dhruti Vasudev Dalal
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Patent number: 10526588Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, 1295, Y342, T343, I357, S360, L361, I363, S365, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: GrantFiled: May 10, 2016Date of Patent: January 7, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Cleoma Arnold, Charles Wayan Schwab, Eileen Thai, Ilya Lederman, Colin Alexander McGaw, Tyler O'Brien Shultz
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Publication number: 20190376133Abstract: The present disclosure provides methods and compositions for enhancing the processivity of a polymerase in catalyzing template-dependent DNA synthesis in high concentrations of salt. Also disclosed are methods and compositions for enhancing the assembly of polymerase-template complex compatible with active DNA synthesis in the presence of low levels of nucleotides and at a high temperature, such as temperatures at or near the melting temperature of the polymerase.Type: ApplicationFiled: July 8, 2019Publication date: December 12, 2019Applicant: Roche Sequencing Solutions, Inc.Inventors: Aruna Ayer, Preethi Sarvabhowman, Charles Schwab
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Publication number: 20190249154Abstract: Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365Q, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, 1644, T647, I648, T651, 1652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.Type: ApplicationFiled: April 29, 2019Publication date: August 15, 2019Inventors: Aruna Ayer, Cleoma Renetta Arnold, Arkadiusz Bibillo, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin Alexander McGaw, Charles Wayan Schwab, Tyler O'Brien Shultz, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Daniel Wunderlich
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Publication number: 20190241952Abstract: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.Type: ApplicationFiled: November 26, 2018Publication date: August 8, 2019Inventors: Aruna Ayer, Peter J. Crisalli, Dmitriy Gremyachinskiy, Meng Taing
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Publication number: 20190225952Abstract: The present disclosure provides variant Pol6 polymerase polypeptides, compositions comprising the Pol6 variant polypeptides, and methods for using the variant Pol6 polypeptides for determining the sequencing of nucleic acids, for example, by nanopore sequencing. The variant Pol6 polymerases possess decreased rates of dissociation of template from the polymerase-template complex, which result in increased processivity relative to the parental Pol6 polypeptides from which they are derived.Type: ApplicationFiled: March 19, 2019Publication date: July 25, 2019Inventors: Evan Amato, Cleoma Arnold, Aruna Ayer, Mara Boenitz-Dulat, Barbara Eckert, Ilya Lederman, Colin McGaw, Preethi Sarvabhowman, Charles Wayan Schwab, Shawn Suko, Eileen Thai, Bigna Woersdoerfer, David Wunderlich
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Publication number: 20190177706Abstract: Described herein are polymerase variants that are exonuclease deficient. Some variants retain the strand displacement capability comparable to the wild-type or parental polymerase. Some variants have a strand displacement capability that is improved relative to the wild-type or parental polymerase. The variants may have an extension rate that is greater than the wild-type or parental polymerase. The variants may have a waiting time that is less than the wild-type or parental polymerase.Type: ApplicationFiled: February 20, 2019Publication date: June 13, 2019Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
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Patent number: 10308918Abstract: Described herein are variant pol6 polymerase having at least having at least two substitutions, wherein at least one of the substitutions is at position S366 of SEQ ID NO: 2. The disclosed polymerases may be coupled to alpha-hemolysin nanopores, and may be used in nanopore-based sequencing apparatuses.Type: GrantFiled: February 1, 2016Date of Patent: June 4, 2019Assignees: Roche Molecular Systems, Inc., Genia Technologies, Inc.Inventors: Aruna Ayer, Arkadiusz Bibillo, Cleoma Renetta Arnold, Charles Wayan Schwab, Eileen Thai, Ilya Lederman, Colin Alexander McGaw, Tyler O'Brien Shultz, Barbara Eckert, Shawn Suko, Mara Boenitz-Dulat, Bigna Woersdoerfer, David Daniel Wunderlich
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Patent number: 10266813Abstract: Described herein are polymerase variants that are exonuclease deficient. Some variants retain the strand displacement capability comparable to the wild-type or parental polymerase. Some variants have a strand displacement capability that is improved relative to the wild-type or parental polymerase. The variants may have an extension rate that is greater than the wild-type or parental polymerase. The variants may have a waiting time that is less than the wild-type or parental polymerase.Type: GrantFiled: February 27, 2017Date of Patent: April 23, 2019Assignee: Genia Technologies, Inc.Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai