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).

  • Patent number: 10851353
    Abstract: 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: Grant
    Filed: March 19, 2019
    Date of Patent: December 1, 2020
    Assignees: 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
  • Patent number: 10829747
    Abstract: 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: Grant
    Filed: September 20, 2017
    Date of Patent: November 10, 2020
    Assignees: 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
  • Publication number: 20200283842
    Abstract: 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: Application
    Filed: February 21, 2020
    Publication date: September 10, 2020
    Inventors: Aruna AYER, George M. CHURCH, Mirko PALLA, Francios PEPIN, Sukanya Srinivasa Rao Arun PUNTHAMBAKER, Peter B. STRANGES
  • Publication number: 20200277581
    Abstract: 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: Application
    Filed: May 11, 2020
    Publication date: September 3, 2020
    Applicant: 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
  • Publication number: 20200270589
    Abstract: 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: Application
    Filed: May 11, 2020
    Publication date: August 27, 2020
    Applicant: 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
  • Publication number: 20200263248
    Abstract: 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: Application
    Filed: March 18, 2020
    Publication date: August 20, 2020
    Applicant: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Meng Taing, Aruna Ayer, Peter J. Crisalli
  • Publication number: 20200190572
    Abstract: 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: Application
    Filed: February 26, 2020
    Publication date: June 18, 2020
    Inventors: Aruna Ayer, Preethi Sarvabhowman, Dhruti Vasudev Dalal
  • Publication number: 20200190489
    Abstract: 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: Application
    Filed: February 26, 2020
    Publication date: June 18, 2020
    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
  • Patent number: 10655174
    Abstract: 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: Grant
    Filed: May 24, 2017
    Date of Patent: May 19, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Meng Taing, Aruna Ayer, Peter J. Crisalli
  • Patent number: 10612009
    Abstract: 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: Grant
    Filed: April 29, 2019
    Date of Patent: April 7, 2020
    Assignees: 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
  • Publication number: 20200087636
    Abstract: 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: Application
    Filed: November 25, 2019
    Publication date: March 19, 2020
    Inventors: Aruna AYER, Cleoma ARNOLD, Charles Wayan SCHWAB, Eileen THAI, Ilya LEDERMAN, Colin Alexander MCGAW, Tyler O'Brien SHULTZ
  • Patent number: 10590480
    Abstract: 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: Grant
    Filed: February 27, 2017
    Date of Patent: March 17, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Aruna Ayer, Preethi Sarvabhowman, Dhruti Vasudev Dalal
  • Patent number: 10526588
    Abstract: 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: Grant
    Filed: May 10, 2016
    Date of Patent: January 7, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Aruna Ayer, Cleoma Arnold, Charles Wayan Schwab, Eileen Thai, Ilya Lederman, Colin Alexander McGaw, Tyler O'Brien Shultz
  • Publication number: 20190376133
    Abstract: 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: Application
    Filed: July 8, 2019
    Publication date: December 12, 2019
    Applicant: Roche Sequencing Solutions, Inc.
    Inventors: Aruna Ayer, Preethi Sarvabhowman, Charles Schwab
  • Publication number: 20190249154
    Abstract: 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: Application
    Filed: April 29, 2019
    Publication date: August 15, 2019
    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
  • Publication number: 20190241952
    Abstract: 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: Application
    Filed: November 26, 2018
    Publication date: August 8, 2019
    Inventors: Aruna Ayer, Peter J. Crisalli, Dmitriy Gremyachinskiy, Meng Taing
  • Publication number: 20190225952
    Abstract: 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: Application
    Filed: March 19, 2019
    Publication date: July 25, 2019
    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
  • Publication number: 20190177706
    Abstract: 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: Application
    Filed: February 20, 2019
    Publication date: June 13, 2019
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai
  • Patent number: 10308918
    Abstract: 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: Grant
    Filed: February 1, 2016
    Date of Patent: June 4, 2019
    Assignees: 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
  • Patent number: 10266813
    Abstract: 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: Grant
    Filed: February 27, 2017
    Date of Patent: April 23, 2019
    Assignee: Genia Technologies, Inc.
    Inventors: Aruna Ayer, Arkadiusz Bibillo, Preethi Sarvabhowman, Dhruti Vasudev Dalal, Ilya Lederman, Eileen Thai