University of California

Ontera Inc.

Toyota Motor Engineering & Manufacturing North America, Inc.

Brigham Young University

Oxford Nanopore Technologies Limited

Nooma Bio, Inc.

Two Pore Guys, Inc.

William Dunbar

Daniel Branton

David W Deamer

Mark Albert Akeson

Noah A Wilson

Trevor J Morin

Daniel Alexander Heller

Roger Jinteh Arrigo Chen

Derek Stanley Caveney

Xu Liu

Jungsuk Kim

Holger Schmidt

Aaron Roe Hawkins

William McKenna

Kathy Lieberman

Kate Lieberman

Yuning Zhang

Yanan Zhao

Eric Thorne

Michael A Summers

Seico Benner

Kenneth D Pedrotti

Hongyun Wang

Reto Stamm

Robin Abu-Shumays

Nicholas Hurt

Tyler Shropshire

Michael Summers

Seiko L Endo

Provided are methods and compositions for detecting a target molecule or particle suspected to be present in a sample using a polymer scaffold, a fusion molecule, and a pore.

Target detection with nanopore

The present disclosure provides an automated method of mapping one or more features of a target polynucleotide. Also provided in the present disclosure are automated methods for sequencing a polynucleotide sequence. Also provided in the present disclosure are methods of extended recapture of a polynucleotide in a nanopore device. Also provided in the present disclosure are devices and systems for carrying out the methods of the present disclosure.

Logic driven polynucleotide scanning for mapping features in a nanopore device

Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Compositions, devices, systems, and methods for using a nanopore

Disclosed herein are methods and compositions for determining an improved estimate of the fractional abundance of target analytes (e.g., specific polynucleotide sequences) in a sample using a nanopore sensor having one or more nanopores-, e.g., by correcting errors inherent to identifying and correlating electrical signals to amounts of a target analyte or reference analyte in a sample.

Multipore determination of fractional abundance of polynucleotide sequences in a sample

Disclosed herein are methods and compositions for determining an improved estimate of the true fractional abundance of target analytes (e.g., specific polynucleotide sequences) in a sample using a nanopore sensor, e.g., by correcting errors inherent to identifying and correlating electrical signals to amounts of a target analyte or reference analyte in a sample.

Fractional abundance of polynucleotide sequences in a sample

Two-pore devices and method for sequencing are described. A two-pore device can include first chamber, a second chamber, and a third chamber, wherein the first chamber is in communication with the second chamber through a first nanopore, and wherein the second chamber is in communication with the third chamber through a second nanopore. The device can also include sensing circuitry for measuring electrical signals associated with a target at a nanopore, and control circuitry for controlling motion of the target at a nanopore. The device can include and/or switch between sensing and control modes for each of the first nanopore and the second nanopore. Sequencing methods can implement a two-pore device in relation to translocation of a target through one or more nanopores, switching between sensing and control modes as appropriate, and measuring aspects of the target using in sensing modes.

Dual pore&#x2014;control and sensor device

Disclosed herein are methods and compositions for detection of target polynucleotides in a mixed sample by amplification of the target polynucleotide and detection in a nanopore device.

Nanopore detection of target polynucleotides from sample background

Provided is a device comprising a channel through and defined by a plurality of layers surrounding the channel, the channel connecting a first and a second chambers separated by the plurality of layers, wherein the plurality of layers comprise a first layer, a second layer; and a conductive middle layer disposed between the first and second layers, wherein the channel comprises (a) a first region defined by the first layer, denoted as an inlet, that is about 0.5 nm to about 100 nm in diameter and (b) a second region defined by the second layer, denoted as an outlet, wherein the inlet and the outlet are about 10 nm to about 1000 nm apart from each other, and wherein the first and second chambers and the middle layer are connected to a power supply. Also provided are methods of preparing and using the device, in particular for nucleic acid sequencing.

Two-chamber dual-pore device

Described herein are nanopore devices as well as methods for assembling a nanopore device including one or more nanopores that can be used to detect molecules such as nucleic acids, amino acids (proteins), and the like. Specifically, a nanopore device includes an insulating layer that reduces electrical noise and thereby improves the sensing resolution of the one or more nanopores integrated within the nanopore device.

Wafer-scale assembly of insulator-membrane-insulator devices for nanopore sensing

Provided are methods for detecting a target molecule or particle suspected to be present in a sample, comprising (a) contacting the sample with (i) a fusion molecule comprising a ligand capable of binding to the target molecule or particle and a binding domain, and (ii) a polymer scaffold comprising at least one binding motif to which the binding domain is capable of binding, under conditions that allow the target molecule or particle to bind to the ligand and the binding domain to bind to the binding motif; (b) loading the polymer into a device comprising a pore that separates an interior space of the device into two volumes, and configuring the device to pass the polymer through the pore from one volume to the other volume, wherein the device further comprises a sensor adjacent to the pore configured to identify objects passing through the pore; and (c) determining, with the sensor, whether the fusion molecule or particle bound to the binding motif is bound to the target molecule or particle, thereby detecting the presence of the target molecule or particle in the sample.

Target detection with nanopore and a polymer scaffold complex

Distributed control of vehicles with coordinating cars that implement a cooperative control method, and non-coordinating cars that are presumed to follow predictable dynamics. A cooperative control method can combine distributed receding horizon control, for optimization-based path planning and feedback, with higher level logic, to ensure that implemented plans are collision free. The cooperative method can be completely distributed with partially synchronous execution, and can afford dedicated time for communication and computation, features that are prerequisites for implementation on real freeways. The method can test for conflicts and can calculate optimized trajectories by adjusting parameters in terminal state constraints of an optimal control problem.

Cooperative driving and collision avoidance by distributed receding horizon control

Devices and methods for detecting a target molecule are provided herein. The methods entail contacting a sample with a polymer scaffold, the polymer comprising at least one association site configured to associate with the target molecule. The sample is brought into contact with the polymer to determine whether the target molecule is present in the sample under conditions allowing the target molecule, if present, to associate with the polymer scaffold. The methods further involve loading the polymer into a device comprising a pore or channel that connects two volumes, configuring the device to pass the polymer through the pore or channel from one volume to the other volume, and determining, with a sensor configured to detect objects passing through the pore or channel, whether the target molecule is associated with the association site, and thereby detecting the presence or absence of the target molecule in the sample.

Multiplexed biomarker quantitation by nanopore analysis of biomarker-polymer complexes

Growing community of inventors

Santa Cruz, CA, United States of America

William Dunbar