Caribou Biosciences, Inc.

Fluidigm Corporation

Pioneer Hi-bred International, Inc.

Mds Sciex

Ceribou Biosciences, Inc.

General Electric Company

Andrew Paul May

Paul Daniel Donohoue

Rachel E Haurwitz

Jing Wang

Peilin Chen

Jennifer A Doudna

Matthew Merrill Carter

Megan Anderson

Marc Alexander Unger

Bernhard Zimmermann

Brian Fowler

Fiona Kaper

Robert C Jones

James M Berger

David S Cohen

Jason A A West

Jake Kimball

Jun Wang

Dominique Toppani

Myo Thu Maung

Ronald Lebofsky

Michael C Norris

Hany Ramaz Nassef

John Van Der Oost

Martin Pieprzyk

Kim Huat Lee

Jun Yan

Ming Fang Zhou

Seng Beng Ng

Megan Van Overbeek

Daniël Christianus Swarts

Hou-Pu Chou

Michael Ybarra Lucero

Yuri Alexeyevich Plotnikov

Changting Wang

David J Balaban

Hany Ramez Nassef

Igor A Shmulevich

Antoine Daridon

Alain Mir

Peter Sean Cameron

Ramesh Ramakrishnan

Paul Wyatt

Robert G Chapman

Kathy Yokobata

Pejman Ghanouni

Joseph A Heanue

Paul Daniel Donohue

Daniel Capurso

Nikolai Sharkov

Christopher H Nye

Shridhar Nath

Paul Donohoue

Dominique G Toppani

Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.

Nucleic acid encoding reactions

In certain embodiments, the present invention provides amplification methods in which nucleotide tag(s) and, optionally, a barcode nucleotide sequence are added to target nucleotide sequences. In other embodiments, the present invention provides a microfluidic device that includes a plurality of first input lines and a plurality of second input lines. The microfluidic device also includes a plurality of sets of first chambers and a plurality of sets of second chambers. Each set of first chambers is in fluid communication with one of the plurality of first input lines. Each set of second chambers is in fluid communication with one of the plurality of second input lines. The microfluidic device further includes a plurality of first pump elements in fluid communication with a first portion of the plurality of second input lines and a plurality of second pump elements in fluid communication with a second portion of the plurality of second input lines.

Multi-primer amplification method for barcoding of target nucleic acids

The present disclosure provides engineered polynucleotide sequences that form scaffolds and nucleoprotein complexes comprising such engineered polynucleotide sequences that form scaffolds and nucleic acid binding proteins. Nucleic acid sequences encoding the engineered polynucleotide sequences that form scaffolds, as well as expression cassettes, vectors and cells comprising such polynucleotide sequences, are described. A variety of methods for making and using the engineered polynucleotide sequences that form scaffolds are also disclosed.

Engineered nucleic acid-targeting nucleic acids

The present disclosure provides DNA-guided CRISPR systems; polynucleotides comprising DNA, RNA and mixtures thereof for use with CRISPR systems; and methods of use involving such polynucleotides and DNA-guided CRISPR systems.

Methods of use of CRISPR CPF1 hybrid DNA/RNA polynucleotides

This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof.

Compositions and methods of nucleic acid-targeting nucleic acids

CRISPR hybrid DNA/RNA polynucleotides and methods of use

The present disclosure provides engineered cross-type-nucleic-acid targeting nucleic acids and compositions thereof. Nucleic acid sequences encoding the engineered cross-type-nucleic-acid targeting nucleic acids, as well as expression cassettes, vectors and cells comprising such nucleic acid sequences, are described. Also, methods are disclosed for making and using the engineered cross-type-nucleic-acid targeting nucleic acids and compositions thereof.

Engineered nucleic-acid targeting nucleic acids

Methods for gene editing and predicting non-random editing events are described. The methods use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems to characterize and manipulate DNA repair outcomes at Cas-initiated double-strand breaks (DSBs) to anticipate functional outcomes.

Methods for using DNA repair for cell engineering

The present specification discloses engineered Type II CRISPR-Cas9 systems comprising split-nexus Cas9-associated polynucleotides (sn-casPNs), including systems comprising three split-nexus Cas9-associated polynucleotides (sn1-casPN/sn2-casPN/sn3-casPN) and systems comprising two split-nexus Cas9-associated polynucleotides (sn1-casPN/sn2-casPN). Together with a Cas9 protein, the sn-casPNs facilitate site-specific modifications, including cleavage and mutagenesis, of a target polynucleotide in vitro and in vivo. Furthermore, the engineered Type II CRISPR-Cas9 systems comprising sn-casPNs are useful in methods of regulating expression of a target nucleic acid. Methods are described herein for the creation of a variety of engineered Type II CRISPR-Cas9 systems comprising two or more sn-casPNs. Polynucleotide sequences, expression cassettes, vectors, compositions, and kits for carrying out a variety of methods are also described. Furthermore, the present specification provides genetically modified cells, compositions of modified cells, transgenic organisms, pharmaceutical compositions, as well as a variety of compositions and methods involving the engineered Type II CRISPR-Cas9 systems.

Compositions and methods of engineered CRISPR-Cas9 systems using split-nexus Cas9-associated polynucleotides

The present disclosure provides engineered Class 2 CRISPR-Cas-associated discontinuous first-stem nucleic-acid targeting nucleic acids, nucleoprotein complexes comprising these nucleic acids, and compositions thereof. Nucleic acid sequences encoding the Class 2 CRISPR-Cas-associated discontinuous first-stem nucleic-acid targeting nucleic acids, as well as expression cassettes, vectors and cells comprising such nucleic acid sequences, are described. Also, methods are disclosed for making and using the Class 2 CRISPR-Cas-associated discontinuous first-stem nucleic-acid targeting nucleic acids, nucleoprotein complexes comprising such nucleic acids, and compositions thereof.

Method of target cleaving using CRISPR hybrid DNA/RNA polynucleotides

Cells containing CRISPR hybrid DNA/RNA polynucleotides

Growing community of inventors

San Francisco, CA, United States of America

Andrew Paul May