Patents by Inventor Benjamin A. Flusberg
Benjamin A. Flusberg 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: 11844666Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: March 23, 2023Date of Patent: December 19, 2023Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Publication number: 20230268029Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: March 23, 2023Publication date: August 24, 2023Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Publication number: 20230268030Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: March 23, 2023Publication date: August 24, 2023Inventors: Benjamin Flusberg, Jonas Korlach, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Dale Webster, Jeremiah Hanes
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Publication number: 20230148447Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: August 26, 2020Publication date: May 11, 2023Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
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Publication number: 20220023049Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: August 26, 2020Publication date: January 27, 2022Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
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Patent number: 11067562Abstract: The invention relates to methods for nanopore sequencing. A substrate such as a semiconductor is provided having a nanopore or an array of nanopores connecting an upper solution with a lower solution. A polymerase-nucleic acid complex comprising a strand displacing DNA polymerase and a circular nucleic acid template and components required for DNA synthesis are provided. The polymerase produces a nascent DNA strand complementary to the circular nucleic acid template and this nascent strand is translocated through the nanopore while it is being produced by a polymerase-nucleic acid complex comprising a strand displacing DNA polymerase and a circular nucleic acid template and providing the components required for DNA synthesis whereby the polymerase produces a nascent DNA strand which is translocated through the nanopore while the nascent DNA strand is being produced. The sequence of the nascent DNA strand is determined while it translates through the pore using the measured current over time.Type: GrantFiled: September 18, 2019Date of Patent: July 20, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 10793903Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: September 28, 2016Date of Patent: October 6, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
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Publication number: 20200141918Abstract: The invention relates to methods for nanopore sequencing. A substrate such as a semiconductor is provided having a nanopore or an array of nanopores connecting an upper solution with a lower solution. A polymerase-nucleic acid complex comprising a strand displacing DNA polymerase and a circular nucleic acid template and components required for DNA synthesis are provided. The polymerase produces a nascent DNA strand complementary to the circular nucleic acid template and this nascent strand is translocated through the nanopore while it is being produced by a polymerase-nucleic acid complex comprising a strand displacing DNA polymerase and a circular nucleic acid template and providing the components required for DNA synthesis whereby the polymerase produces a nascent DNA strand which is translocated through the nanopore while the nascent DNA strand is being produced. The sequence of the nascent DNA strand is determined while it translates through the pore using the measured current over time.Type: ApplicationFiled: September 18, 2019Publication date: May 7, 2020Inventors: Stephen Turner, Benjamin Flusberg
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Publication number: 20190360997Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow, or kinetically observable kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 5:1 to 1:5. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.Type: ApplicationFiled: April 8, 2019Publication date: November 28, 2019Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 10481144Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides devices having an array of nanopores. The devices comprise an upper fluidic region in fluidic contact with the nanopores. The upper fluidic region comprises and upper electrode. Below each nanopore, and in fluidic contact with each nanopore is a discrete fluidic region. There is no direct fluidic contact between these discrete fluidic regions. The devices have an advantage of lower levels of electrical cross-talk between nanopores in the array for improved nucleic acid sequencing.Type: GrantFiled: July 19, 2017Date of Patent: November 19, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 10473639Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow, or kinetically observable kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 5:1 to 1:5. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.Type: GrantFiled: April 8, 2019Date of Patent: November 12, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 10294523Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: GrantFiled: September 23, 2015Date of Patent: May 21, 2019Assignee: Pacific Biosciences of California, Inc.Inventors: Benjamin Flusberg, Jonas Korlach, Jeffrey Wegener, Tyson A. Clark, Igor Drasko Vilfan, Andrey Kislyuk, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner, Austin B. Tomaney, Patrick Marks, Jessica Lee, Lei Jia, Dale Webster, John Lyle, Jeremiah Hanes
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Publication number: 20190133449Abstract: Analysis of live beings is facilitated. According to an example embodiment of the present invention, a light-directing arrangement such as an endoscope is mounted to a live being. Optics in the light-directing arrangement are implemented to pass source light (e.g., laser excitation light) into the live being, and to pass light from the live being for detection thereof. The light from the live being may include, for example, photons emitted in response to the laser excitation light (i.e., fluoresced). The detected light is then used to detect a characteristic of the live being.Type: ApplicationFiled: September 24, 2018Publication date: May 9, 2019Inventors: Benjamin A. Flusberg, Eric David Cocker, Juergen Claus Jung, Mark J. Schnitzer
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Patent number: 9993794Abstract: Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. For example, methods are presented for providing a surface comprising the plurality of array regions by exposing the surface to a solution comprising polymerase enzymes where each polymerase enzyme is bound to a binding structure having several functional moieties. The functional moieties of the binding structure react with the binding elements on the array regions such that the functional moieties on the binding structure react with other available binding sites in an array region, preventing other polymerase-binding structures from loading, and resulting in a single polymerase molecule bound to each of these regions.Type: GrantFiled: November 4, 2014Date of Patent: June 12, 2018Assignee: Paciic Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg, Lei Sun
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Publication number: 20180074040Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides devices having an array of nanopores. The devices comprise an upper fluidic region in fluidic contact with the nanopores. The upper fluidic region comprises and upper electrode. Below each nanopore, and in fluidic contact with each nanopore is a discrete fluidic region. There is no direct fluidic contact between these discrete fluidic regions. The devices have an advantage of lower levels of electrical cross-talk between nanopores in the array for improved nucleic acid sequencing.Type: ApplicationFiled: July 19, 2017Publication date: March 15, 2018Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 9772323Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides for using the signals from N monomeric units (n-mers) within the nanopore to provide sequence information. The invention includes substrates having arrays of nanopores with incorporated electronic circuits, for example, in semiconductor substrates. In some cases, the arrays of nanopores reside in discrete reservoirs.Type: GrantFiled: February 22, 2017Date of Patent: September 26, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 9746476Abstract: The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.Type: GrantFiled: June 10, 2015Date of Patent: August 29, 2017Assignee: Pacific Biosciences of California, Inc.Inventors: Jonas Korlach, Stephen Turner, Benjamin Flusberg, Mark Chaisson, Eric Schadt, Jeffrey Wegener
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Publication number: 20170233802Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: September 28, 2016Publication date: August 17, 2017Inventors: Benjamin Flusberg, Stephen Turner, Jon Sorenson, Kevin Travers, Cheryl Heiner
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Publication number: 20170168040Abstract: The invention relates to devices and methods for nanopore sequencing. The invention provides for using the signals from N monomeric units (n-mers) within the nanopore to provide sequence information. The invention includes substrates having arrays of nanopores with incorporated electronic circuits, for example, in semiconductor substrates. In some cases, the arrays of nanopores reside in discrete reservoirs.Type: ApplicationFiled: February 22, 2017Publication date: June 15, 2017Inventors: Stephen Turner, Benjamin Flusberg
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Patent number: 9678056Abstract: The invention relates to devices and methods for nanopore sequencing. Methods for controlling translocation of through the nanopore are disclosed. The rate of transport of the template nucleic acids through the nanopore can be controlled using a translocating enzyme having two slow kinetic steps. The translocating enzyme and reaction conditions can be selected such that the translocating enzyme exhibits two kinetic steps wherein each of the kinetic steps has a rate constant, and the ratio of the rate constants of the kinetic steps is from 10:1 to 1:10. The invention also provides for using the signals from n-mers to provide sequence information, for example where the system has less than single base resolution. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS.Type: GrantFiled: December 1, 2016Date of Patent: June 13, 2017Assignee: Pacific Biosciense of California, Inc.Inventors: Stephen Turner, Benjamin Flusberg