Patents Assigned to Pacific Biosciences of California, Inc.
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Publication number: 20210147928Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.Type: ApplicationFiled: August 28, 2020Publication date: May 20, 2021Applicant: Pacific Biosciences of California, Inc.Inventors: Lubomir SEBO, Gene SHEN, Stephen YUE, Honey OSUNA, Yuri LAPIN, Louis BROGLEY, Andrei FEDOROV
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Publication number: 20210147465Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.Type: ApplicationFiled: August 28, 2020Publication date: May 20, 2021Applicant: Pacific Biosciences of California, Inc.Inventors: Lubomir SEBO, Jeremiah HANES, Gene SHEN, Louis BROGLEY, Stephen YUE, Frank ZHENG, Yuri LAPIN, John LYLE, Honey OSUNA, Andrei FEDOROV
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Patent number: 11001889Abstract: An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.Type: GrantFiled: November 26, 2018Date of Patent: May 11, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Adrian Fehr, Nathaniel Joseph McCaffrey, Stephen Turner
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Publication number: 20210124115Abstract: Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.Type: ApplicationFiled: September 4, 2020Publication date: April 29, 2021Applicant: Pacific Biosciences of California, Inc.Inventors: Ravi SAXENA, Michael Tzu RU, Takashi Whitney ORIMOTO, Annette GROT, Mathieu FOQUET, Hou-Pu CHOU
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Patent number: 10975362Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: November 6, 2018Date of Patent: April 13, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Lei Jia, Robin Emig, Erik Miller, Walter H. Lee
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Patent number: 10968482Abstract: This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.Type: GrantFiled: May 18, 2020Date of Patent: April 6, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Cheng Frank Zhong, Paul Lundquist, Mathieu Foquet, Jonas Korlach, Hovig Bayandorian
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Patent number: 10954496Abstract: 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.Type: GrantFiled: March 15, 2019Date of Patent: March 23, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Jeremiah Hanes
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Patent number: 10948652Abstract: Provided herein are systems, devices, and methods for improved optical waveguide transmission and alignment in an analytical system. Waveguides in optical analytical systems can exhibit variable and increasing back reflection of single-wavelength illumination over time, thus limiting their effectiveness and reliability. The systems are also subject to optical interference under conditions that have been used to overcome the back reflection. Novel systems and approaches using broadband illumination light with multiple longitudinal modes have been developed to improve optical transmission and analysis in these systems. Novel systems and approaches for the alignment of a target waveguide device and an optical source are also disclosed.Type: GrantFiled: November 3, 2018Date of Patent: March 16, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Alexey Kuritsyn, Mark McDonald, Aaron Rulison, Russell Berman
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Patent number: 10941443Abstract: Real time redox sequencing methods, devices, and systems are described. Arrays of redox devices comprising one or two electrodes are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the electrode(s). A sequencing reaction mixture comprising nucleotide analogs comprising redox labels is introduced to the array of redox devices under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by electrochemically identifying the redox labels of the nucleotide analogs that are incorporated into the growing strand.Type: GrantFiled: March 18, 2019Date of Patent: March 9, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Jonas Korlach, Stephen Turner, Lei Sun
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Patent number: 10934585Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.Type: GrantFiled: June 13, 2018Date of Patent: March 2, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
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Patent number: 10934583Abstract: 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.Type: GrantFiled: December 8, 2017Date of Patent: March 2, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Stephen Turner, Jeremiah Hanes, Keith Bjornson
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Patent number: 10920268Abstract: The present disclosure provides improved methods for isolating asymmetrically-primed and/or asymmetrically-tagged nucleic acid complexes that find use in downstream analytical analyses, including sequence analysis. Compositions comprising such complexes and kits and systems for generating such complexes are also provided.Type: GrantFiled: July 16, 2018Date of Patent: February 16, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Lei Sun, Sassan Sheikholeslami, Natasha Popovich, David Christopher Scherer
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Publication number: 20210033788Abstract: Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.Type: ApplicationFiled: July 10, 2020Publication date: February 4, 2021Applicant: Pacific Biosciences of California, Inc.Inventors: Shang WANG, Mathieu FOQUET, Paul LUNDQUIST, Aaron RULISON, Mark MCDONALD, Ariel HERRMANN
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Patent number: 10901145Abstract: The application relates to methods of analyzing luminescent species. A substrate is provided that has a plurality of zero mode waveguides having apertures that extend through an upper non-reflective layer that is disposed on a lower transparent layer of a substrate. The apertures have non-reflective oxide layers on the reflective side walls of the apertures, the side walls having a thickness of greater than 10 nm, and the oxide layer is formed by oxidizing the non-reflective layer. The volume within the oxide layer defines a solution volume, and the volume within the reflective walls defines a ZMW volume. Having such non-reflective layers on the walls of the ZMW usefully decouples the solution volume from the ZMW volume.Type: GrantFiled: November 27, 2018Date of Patent: January 26, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Jeremy Gray, Lei Sun
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Patent number: 10888832Abstract: The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution.Type: GrantFiled: November 21, 2019Date of Patent: January 12, 2021Assignee: Pacific Biosciences of California, Inc.Inventors: Lei Sun, Natasha Popovich, Gene Shen, Thang Pham, Stephen Turner
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Patent number: 10859497Abstract: Arrays of integrated analytical devices and their methods for production are provided. The arrays are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices include an integrated diffractive beam shaping element that provides for the spatial separation of light emitted from the optical reactions.Type: GrantFiled: March 14, 2019Date of Patent: December 8, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Annette Grot, Ravi Saxena, Paul Lundquist
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Patent number: 10858651Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.Type: GrantFiled: August 28, 2019Date of Patent: December 8, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Yu-Chih Tsai, Igor Vilfan, Khai Luong
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Patent number: 10814299Abstract: Methods, compositions, and systems for distributing nucleic acids into array regions are provided. The methods, compositions, and systems utilize nucleic acid condensing agents to increase efficiency of distribution of the nucleic acids into the array regions. Various methods for facilitating distribution of the nucleic acids to the array regions are provided.Type: GrantFiled: November 17, 2016Date of Patent: October 27, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Lei Sun, Jaime Juan Benitez-Marzan, Natasha Popovich, Sassan Sheikholeslami, Steven Lin, Aparna Vedula
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Patent number: 10815465Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties include increased resistance to photodamage, and can also include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: June 7, 2019Date of Patent: October 27, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Satwik Kamtekar, Arek Bibillo, Keith Bjornson, Fred Christians, Colleen Cutcliffe, Jeremiah Hanes, Lei Jia, Walter Lee, Erik Miller, Pranav Patel
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Patent number: 10800805Abstract: Protected fluorescent reagent compounds and their methods of synthesis are provided. The compounds are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The compounds contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements.Type: GrantFiled: April 30, 2018Date of Patent: October 13, 2020Assignee: Pacific Biosciences of California, Inc.Inventors: Lubomir Sebo, Jeremiah Hanes, Gene Shen, Louis Brogley, Stephen Yue, Frank Zheng, Yuri Lapin, John Lyle, Honey Osuna, Andrei Fedorov