公开(公告)号：US11718639B2

公开(公告)日：2023-08-08

申请号：US17230007

申请日：2021-04-14

Applicant: Pacific Biosciences of California, Inc.

Inventor： Keith Bjornson ,  Jeremiah Hanes ,  Erik Miller ,  Satwik Kamtekar ,  Lubomir Sebo ,  Louis Brogley

IPC: C07H21/04 ,  C07H19/06 ,  C07H19/16 ,  G01N33/58 ,  C07K14/36 ,  C12Q1/6874 ,  C12N9/10 ,  C09B23/08 ,  C09B69/10 ,  C12Q1/6869

CPC classification number: C07H21/04 ,  C07H19/06 ,  C07H19/16 ,  C07K14/36 ,  C09B23/083 ,  C09B69/105 ,  C12N9/10 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N33/582 ,  G01N33/583 ,  C12Q2523/313 ,  C12Q2535/113 ,  C12Q2563/107 ,  C12Q2563/131 ,  C12Q1/6874 ,  C12Q2523/313 ,  C12Q2563/107 ,  C12Q2563/131 ,  C12Q1/6869 ,  C12Q2535/113 ,  C12Q2563/107

Abstract: Compositions, methods, and systems are provided for fluorescent polymerase enzyme substrates comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Fluorescent polymerase enzyme substrates of the invention have a protein shield between the fluorescent dye moieties and nucleotide moieties of the polymerase enzyme substrate. The polymerase enzyme substrates have a nucleotide component and a dye component, each attached to a protein. The attachments can be covalent. The protein can, for example, prevent the direct interaction of the fluorescent dye moiety with the enzyme when carrying out nucleotide synthesis, preventing photodamage to the enzyme. The polymerase enzyme substrates of the invention can have multiple dyes and multiple nucleotide moieties.

公开(公告)号：US20230010287A1

公开(公告)日：2023-01-12

申请号：US17859770

申请日：2022-07-07

Applicant: Pacific Biosciences of California, Inc.

Inventor： Jeremiah Hanes ,  Robert H. Reamey ,  Lin Wang ,  Fabian Block ,  Kurt Patterson ,  Brittany Ann Rohrman ,  Andrew Sparks ,  Evan Hurowitz ,  Joan Wilson ,  Min-Jui Richard Shen

IPC: C12Q1/6869

Abstract: The present invention provides methods and compositions for carrying out nucleic acid sequencing, particularly paired-end sequencing. The methods use concatemeric sequencing templates that can be produced by rolling circle amplification of asymmetric circular nucleic acids having a central double-stranded region comprising a target nucleic acid sequence that is connected at each end to form a circular construct.

公开(公告)号：US11014958B2

公开(公告)日：2021-05-25

申请号：US16012428

申请日：2018-06-19

Applicant: Pacific Biosciences of California, Inc.

Inventor： Keith Bjornson ,  Jeremiah Hanes ,  Erik Miller ,  Satwik Kamtekar ,  Lubomir Sebo ,  Louis Brogley

IPC: C07H21/04 ,  C12Q1/68 ,  G01N33/58 ,  C07K14/36 ,  C07H19/06 ,  C07H19/16 ,  C12Q1/6874 ,  C12N9/10 ,  C09B23/08 ,  C09B69/10 ,  C12Q1/6869

Abstract: Compositions, methods, and systems are provided for fluorescent polymerase enzyme substrates comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Fluorescent polymerase enzyme substrates of the invention have a protein shield between the fluorescent dye moieties and nucleotide moieties of the polymerase enzyme substrate. The polymerase enzyme substrates have a nucleotide component and a dye component, each attached to a protein. The attachments can be covalent. The protein can, for example, prevent the direct interaction of the fluorescent dye moiety with the enzyme when carrying out nucleotide synthesis, preventing photodamage to the enzyme. The polymerase enzyme substrates of the invention can have multiple dyes and multiple nucleotide moieties.

公开(公告)号：US10934583B2

公开(公告)日：2021-03-02

申请号：US15836736

申请日：2017-12-08

Applicant: Pacific Biosciences of California, Inc.

Inventor： Stephen Turner ,  Jeremiah Hanes ,  Keith Bjornson

IPC: C12Q1/6874 ,  C12Q1/6823 ,  G01N27/22

Abstract: Sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising two electrodes separated by an insulating layer are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the insulating region. A sequencing reaction mixture comprising nucleotide analogs having impedance labels is introduced to the array of nanoscale electronic elements under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance.

公开(公告)号：US10655168B2

公开(公告)日：2020-05-19

申请号：US16230480

申请日：2018-12-21

Applicant: Pacific Biosciences of California, Inc.

Inventor： Satwik Kamtekar ,  Lubomir Sebo ,  Leewin Chern ,  Thomas Linsky ,  Jeremiah Hanes ,  Erik Miller ,  Ying Yang ,  Stephen Yue

IPC: C12Q1/6848 ,  C12N9/22 ,  C07K14/36

Abstract: Compositions comprising covalently modified and mutated biotin-binding proteins, particularly biotin-binding proteins having a negative charge at physiological pH, are provided. Methods of producing such proteins are also provided, as are methods of immobilizing, sequencing, and making nucleic acids employing such proteins.

公开(公告)号：US10544449B2

公开(公告)日：2020-01-28

申请号：US15399931

申请日：2017-01-06

Applicant: Pacific Biosciences of California, Inc.

Inventor： Gene Shen ,  Natasha Popovich ,  Erik Miller ,  Satwik Kamtekar ,  Keith Bjornson ,  Jeremiah Hanes ,  Stephen Yue ,  Lubomir Sebo ,  Zhong Wang

IPC: C07D495/04 ,  C07D403/14 ,  C07D401/14 ,  C12Q1/6844 ,  C08G65/334 ,  C07F7/18

Abstract: Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.

公开(公告)号：US20200002765A1

公开(公告)日：2020-01-02

申请号：US16456867

申请日：2019-06-28

Applicant: Pacific Biosciences of California, Inc.

Inventor： Jaime Juan Benitez-Marzan ,  Natasha Popovich ,  Lei Sun ,  Satwik Kamtekar ,  Keith Bjornson ,  Jeremiah Hanes ,  Karl Voss ,  Erik Miller ,  Thomas Linsky ,  Leewin Chern

IPC: C12Q1/6874 ,  B01J19/00

Abstract: The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in loading of polymerase enzyme complexes into a predetermined number of reaction sites, including nanoscale wells.

公开(公告)号：US20190352621A1

公开(公告)日：2019-11-21

申请号：US16354878

申请日：2019-03-15

Applicant: Pacific Biosciences of California, Inc.

Inventor： Satwik Kamtekar ,  Jeremiah Hanes

IPC: C12N9/12 ,  C12M1/42 ,  C12Q1/6869 ,  C12P19/34

Abstract: Provided are compositions comprising recombinant polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for sequencing RNA or RNA/DNA templates. Polymerases that topologically encircle the template nucleic acid are provided. Also provided are methods of using such polymerases to make a DNA or to sequence a template comprising RNA.

公开(公告)号：US20190194741A1

公开(公告)日：2019-06-27

申请号：US16218280

申请日：2018-12-12

Applicant: Pacific Biosciences of California, Inc.

Inventor： Andrei Fedorov ,  John Lyle ,  Keith Bjornson ,  Jeremiah Hanes

IPC: C12Q1/6869

CPC classification number: C12Q1/6869 ,  C12Q2527/125 ,  C12Q2563/137

Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.

公开(公告)号：US10184148B2

公开(公告)日：2019-01-22

申请号：US15480226

申请日：2017-04-05

Applicant: Pacific Biosciences of California, Inc.

Inventor： Andrei Fedorov ,  John Lyle ,  Keith Bjornson ,  Jeremiah Hanes

IPC: C12Q1/68 ,  C12Q1/6869 ,  C07H21/02

Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.