Patents by Inventor Jens H. GUNDLACH
Jens H. GUNDLACH 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: 20240124928Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.Type: ApplicationFiled: April 24, 2023Publication date: April 18, 2024Applicants: University of Washington, The UAB Research FoundationInventors: Jens H. Gundlach, Michael Niederweis, Thomas Z. Butler, Mikhail Pavlenok, Mark A. Troll, Suja Sukumaran
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Publication number: 20240085372Abstract: Methods for nanopore-based protein analysis are provided. The methods address the characterization of a target protein analyte, which has a dimension greater than an internal diameter of the nanopore tunnel, and which is also physically associated with a polymer. The methods further comprise applying an electrical potential to the nanopore system to cause the polymer to interact with the nanopore tunnel. The ion current through the nanopore is measured to provide a current pattern reflective of the structure of the portion of the polymer interacting with the nanopore tunnel. This is used as a metric for characterizing the associated protein that does not pass through the nanopore.Type: ApplicationFiled: September 27, 2023Publication date: March 14, 2024Applicant: University of WashingtonInventors: Jens H. Gundlach, Ian Michael Derrington, Andrew Laszlo, Jonathan Craig, Henry Brinkerhoff
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Patent number: 11913905Abstract: Provided herein are methods and systems pertaining to sequencing units of analytes using nanopores. In general, arresting constructs are used to modify an analyte such that the modified analyte pauses in the opening of a nanopore. During such a pause, an ion current level is obtained that corresponds to a unit of the analyte. After altering the modified analyte such that the modified analyte advances through the opening, another arresting construct again pauses the analyte, allowing for a second ion current level to be obtained that represents a second unit of the analyte. This process may be repeated until each unit of the analyte is sequenced. Systems for performing such methods are also disclosed.Type: GrantFiled: November 24, 2021Date of Patent: February 27, 2024Assignee: University of WashingtonInventors: Jens H. Gundlach, Ian M. Derrington, Marcus D. Collins
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Patent number: 11879155Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.Type: GrantFiled: May 25, 2021Date of Patent: January 23, 2024Assignee: Illumina, Inc.Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
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Publication number: 20240003896Abstract: The current document discusses a detection system comprising a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type, a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal, and an analysis subsystem that determines the types of entities within the target using the signal.Type: ApplicationFiled: September 14, 2018Publication date: January 4, 2024Applicant: lllumina, Inc.Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia, Jens H. Gundlach
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Patent number: 11821033Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.Type: GrantFiled: December 3, 2020Date of Patent: November 21, 2023Assignee: University of WashingtonInventors: Jens H. Gundlach, Andrew Laszlo
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Publication number: 20230250493Abstract: The present disclosure concerns a method for detecting and characterizing a virus comprising the steps of providing a sample to analyze that is likely to contain a virus, extracting and preparing nucleic acids from the sample, sequence-specifically labeling the nucleic acid, e.g. by introducing fluorophores by contacting the nucleic acid with a methyltransferase or by introducing fluorescently labelled nucleotides after treatment with nickase, performing a genomic mapping analysis of the extracted nucleic acids and performing a computational analysis to detect the presence of and characterise at least one virus. The present disclosure also concerns a kit for carrying out the above method.Type: ApplicationFiled: June 25, 2021Publication date: August 10, 2023Inventors: Volker LEEN, Theo LASSER, Johan HOFKENS, Jens H. GUNDLACH
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Patent number: 11634764Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.Type: GrantFiled: December 14, 2020Date of Patent: April 25, 2023Assignees: University of Washington, The UAB Research FoundationInventors: Jens H. Gundlach, Michael Niederweis, Thomas Z. Butler, Mikhail Pavlenok, Mark A. Troll, Suja Sukumaran
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Publication number: 20220366313Abstract: In some embodiments, a computer-implemented method of determining an identity of one or more monomer subunit residues of a polymer analyte is provided, In some embodiments, a raw current signal generated by using a variable voltage to translocate the polymer analyte through a nanopore. In some embodiments, change points are detected in the raw current signal to determine a series of states, In some embodiments, capacitance compensation is performed on the raw current signal for each state to create an ionic current-vs-voltage curve for each state. In some embodiments, the ionic current-vs-voltage curves is converted to conductance-vs-voltage curves. In some embodiments, filtering is performed for the series of states to create a series of filtered states. In some embodiments, the identity of one or more monomer subunit residues of the polymer analyte is determined based on the series of filtered states.Type: ApplicationFiled: February 14, 2020Publication date: November 17, 2022Applicant: University of WashingtonInventors: Jens H. Gundlach, Matthew Noakes, Henry D. Brinkerhoff
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Publication number: 20220251641Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.Type: ApplicationFiled: February 18, 2022Publication date: August 11, 2022Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
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Publication number: 20220164126Abstract: Provided herein are methods and systems pertaining to sequencing units of analytes using nanopores. In general, arresting constructs are used to modify an analyte such that the modified analyte pauses in the opening of a nanopore. During such a pause, an ion current level is obtained that corresponds to a unit of the analyte. After altering the modified analyte such that the modified analyte advances through the opening, another arresting construct again pauses the analyte, allowing for a second ion current level to be obtained that represents a second unit of the analyte. This process may be repeated until each unit of the analyte is sequenced. Systems for performing such methods are also disclosed.Type: ApplicationFiled: November 24, 2021Publication date: May 26, 2022Applicant: University of WashingtonInventors: Jens H. Gundlach, Ian M. Derrington, Marcus D. Collins
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Patent number: 11254981Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.Type: GrantFiled: July 23, 2019Date of Patent: February 22, 2022Assignee: Illumina, Inc.Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
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Patent number: 11187675Abstract: Provided herein are methods and systems pertaining to sequencing units of analytes using nanopores. In general, arresting constructs are used to modify an analyte such that the modified analyte pauses in the opening of a nanopore. During such a pause, an ion current level is obtained that corresponds to a unit of the analyte. After altering the modified analyte such that the modified analyte advances through the opening, another arresting construct again pauses the analyte, allowing for a second ion current level to be obtained that represents a second unit of the analyte. This process may be repeated until each unit of the analyte is sequenced. Systems for performing such methods are also disclosed.Type: GrantFiled: February 14, 2017Date of Patent: November 30, 2021Assignee: University of WashingtonInventors: Jens H. Gundlach, Ian M. Derrington, Marcus D. Collins
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Publication number: 20210355534Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.Type: ApplicationFiled: May 25, 2021Publication date: November 18, 2021Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
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Publication number: 20210189480Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.Type: ApplicationFiled: December 14, 2020Publication date: June 24, 2021Applicants: University of Washington, The UAB Research FoundationInventors: Jens H. Gundlach, Michael Niederweis, Thomas Z. Butler, Mikhail Pavlenok, Mark A. Troll, Suja Sukumaran
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Patent number: 11041196Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.Type: GrantFiled: June 12, 2019Date of Patent: June 22, 2021Assignee: Illumina, Inc.Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
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Publication number: 20210172013Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.Type: ApplicationFiled: December 3, 2020Publication date: June 10, 2021Applicant: University of Washington through its Center for CommercializationInventors: Jens H. Gundlach, Andrew Laszlo
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Publication number: 20210032695Abstract: The present disclosure provides method and systems for improving nanopore-based analyses of polymers. The disclosure provides methods for selectively modifying one or more monomeric subunit(s) of a kind a pre-analyte polymer that results polymer analyte with a modified subunit. The polymer analyte produces a detectable signal in a nanopore-based system. The detectable signal, and/or its deviation from a reference signal, indicates the location of the modified subunit in the polymer analyte and, thus, permits the identification of the subunit at that location in the original pre-analyte polymer.Type: ApplicationFiled: September 22, 2020Publication date: February 4, 2021Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
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Patent number: 10870883Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.Type: GrantFiled: June 1, 2018Date of Patent: December 22, 2020Assignees: University of Washington, The UAB Research FoundationInventors: Jens H. Gundlach, Michael Niederweis, Thomas Z. Butler, Mikhail Pavlenok, Mark A. Troll, Suja Sukumaran
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Patent number: 10858700Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.Type: GrantFiled: August 2, 2013Date of Patent: December 8, 2020Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jens H. Gundlach, Andrew Laszlo