Pacific Biosciences of California, Inc.

Cornell Research Foundation Inc.

Jonas Korlach

Stephen Wilson Turner

Jeffrey Wegener

Tyson A Clark

Harold G Craighead

Kevin Travers

Watt W Webb

John Lyle

Mathieu Foquet

Thang Pham

Paul M Lundquist

Cheng Frank Zhong

Benjamin A Flusberg

David R Rank

Daniel Bernardo Roitman

Jeremiah Hanes

Cheryl Heiner

Paul S Peluso

Keith P Bjornson

Jon M Sorenson

Geoff Otto

Erik Miller

Lei Jia

Lei Sun

Robin A Emig

Patrick Marks

Satwik Kamtekar

Adrian Nielsen Fehr

Geoffrey Alan Otto

Molly Min He

Pranav Patel

Paul Hardenbol

Michael Levene

Hovig Bayandorian

Yue Xu

Eric Schadt

Arunashree Bhamidipati

Eric Olivares

Dale R Webster

Jeffery Wegener

Austin B Tomaney

Yu-Chih Tsai

Harold Ray Lee

Ron L Cicero

Andrey Kislyuk

Jessica Lee

Fred C Christians

Igor D Vilfan

Ronald L Cicero

David Kagen Hanzel

Mark Chaisson

Steven Benjamin Warren

Joseph Puglisi

Robert Sebra

John S Eid

Andrei Fedorov

Arkadiusz Bibillo

Jeremy Gray

Arek Bibillo

Chuan He

Insil Park

Stephen P Dudek

Hans Callebaut

Steven Lin

Bidhan P Chaudhuri

Meni Wanunu

Ravi Dalal

Liang Zhang

Mathieu Foguet

Xingyu Lu

David Hanzel

Steven Warren

John M Lyle

Jake Freudenthal

Kevan Samiee

Methods, compositions, and systems are provided that allow for reliable sequencing of the initial sequence region of a sequence of interest. The methods of the invention allow for more reliable barcoding of subpopulations of nucleic acids to be sequenced.

Delaying real-time sequencing

This invention provides devices for use in various analytical applications including single-molecule analytical reactions. Methods for detecting analytes optically by propagating optical energy by waveguides within a substrate are provided. Analytical devices are provided which have both shallow and deep waveguides in which illumination light is transported through the deep waveguides and coupled into the shallow waveguides. The shallow waveguides provide evanescent field illumination to analytes, such as single-molecule analytes, within nanometer scale wells. Integrated devices including integrated detectors such as CMOS detectors are included.

Substrates and optical systems and methods of use thereof

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.

Classification of nucleic acid templates

Compositions, methods and systems are provided for isolating nucleic acids. A polymerase-nucleic acid complex can be formed by mixing a polymerase enzyme comprising strand displacement activity and a mixture of double stranded nucleic acids. Nucleic acid synthesis can then be initiated by the polymerase enzyme to produce a nascent strand complementary to the first strand, thereby displacing a portion of the second strand. After halting or reducing the rate of nucleic acid synthesis, a hybridizing a hook oligonucleotide can be used hybridize to the nucleic acid through a capture region on the hook oligonucleotide that is complementary to the displaced portion of the second strand. The nucleic acid can then be isolated from the mixture of nucleic acids using the hook oligonucleotide.

Methods for isolating nucleic acids

A circuit comprising a substrate with sectors on the substrate is provided, each sector comprising clock and data lines, a controller in electrical communication with the clock and data lines, a counter bias line, an amplifier input line and nano-electronic measurement devices on the substrate. A source of each device is coupled to the counter bias line and a drain of each device is coupled to the amplifier input line to obtain an electrical signal on the drain, the identity of which is determined by electrical interaction between the device and a charge label. Each device drain is gated by a corresponding switch between an on state, in which the drain is connected to the amplifier input line, and an off state, in which the drain is isolated from the amplifier input line. The controller controls switch states responsive to clock signal line pulses and data input line data.

Systems and methods for selectively addressing sparsely arranged electronic measurement devices

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.

Compositions and methods for selection of nucleic acids

Analytic device comprising a substrate, nanometer-scale wells, and shallow waveguide optically coupled to a deep waveguide

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.

Articles having localized molecules disposed thereon and methods of producing same

Real time electronic sequencing devices, chips, and systems are described. Arrays of nanoFET devices are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound to the nanoFET. The nanoFET devices typically have a source, a drain and a gate comprising a nanowire. A single polymerase enzyme complex comprising a polymerase enzyme complexed with the template nucleic acid is bound to the gate. The polymerase is bound to the gate non-covalently through a polymeric binding agent that has two strands, each strand interacting with the nanowire such that the polymerase is in a central location between the strands with the polymeric binding agent extending away from the polymerase complex along the nanowire in both directions.

Single-molecule nanoFET sequencing systems and methods

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.

Substrates and optical systems and methods of use thereof for performing sequencing by synthesis

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.

Real-time redox sequencing chips

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.

Loading extended polymerase-nucleic acid complexes

Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.

Modular nucleotide compositions and uses therefor

Analytic device comprising a nanohole extending through an opaque mask layer and into a waveguide cladding

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Newark, CA, United States of America

Jonas Korlach