E Ink Corporation

Massachusetts Institute of Technology

Gen9, Inc.

Impossible Objects, Inc.

Other

Whitehead Institute for Biomedical Research

Ginkgo Bioworks, Inc.

The Microoptical Corporation

Joseph M Jacobson

Paul Stephen Drzaic

Jonathan D Albert

Barrett Comiskey

Ian D Morrison

David W Mosley

Barrett O Comiskey

Andrew L Loxley

Michael E Hudson

Daniel Schindler

Libing Zhang

Robert David Feeney

Larry Li-Yang Chu

Peter A Carr

Li-yun A Kung

Brian Yichiun Chow

Senthil Ramu

Christopher Emig

Richard J Paolini, Jr

Thomas Henry Whitesides

Russell J Wilcox

Noah Michael Jakimo

Karl Raymond Amundson

Michael D McCreary

Alexi Arango

Brian N Hubert

Saul Griffith

Vikrant Agnihotri

Martin J Goldberg

Robert W Swartz

Eugene Gore

Buckley Crist

David Kong

Pranam Chatterjee

George M Church

Scott R Manalis

Richard M Webber

Andrew Wilson

Scott S Lawton

Vikas Anant

Ishtiaq E Saaem

Brent Ridley

Ashley Salomon

Will DelHagen

Kie-Moon Sung

Li-Yun A Kung

Robert Waverly Zehner

Gregg Michael Duthaler

Peter T Kazlas

Charles Howie Honeyman

Jian Lin

David Darrell Miller

Bin Wu

Shuguang Zhang

Jianna Wang

Anthony Edward Pullen

Yu Chen

Kevin L Denis

John J Schwartz

Christopher T Turner

Kimberly Hamad

Caprice L Gray

Jonathan Albert

Jae-bum Joo

Jon Varsanik

Neil Adam Gershenfeld

Kimin Jun

Mark B Spitzer

Holly G Gates

V Michael Bove, Jr

David Sabatini

Steven J O'Neil

Glen Crossley

Dirk Hertel

Justin J Abramson

Mavyn M Holman

Katharine Geramita

Emily J Pratt

Stephen F Archer

Babak Nivi

Charles Victor Fracchia

Aggelos Bletsas

Colin A Bulthaup

Eric J Wilhelm

Sophea Sann-Rorth

Ellen J Sanchez

Sawyer Fuller

Hidekazu Yoshizawa

Mike Hudson

Naama Kanarek

Nicholas James Guido

Devin Leake

Andrew Kirk Wilson

Richard Paolini

Robert Feeney

EngineeredCas9 (ScCas9) variants include an ScCas9 protein with its PID being the PID amino acid composition ofCas9 (SpCas9-NG, an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 in its amino acid sequence (Sc+), and an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 and a substitution of residues ADKKLRKRSGKLATE [SEQ ID No. 4] in position 365-379 in the ScCas9 open reading frame (Sc++). Also included are CRISPR-associated DNA endonucleases with a PAM specificity of 5'-NG-3′ or 5′-NNG-3′ and a method of altering expression of a gene product by utilizing the engineered ScCas9 variants.

Applications of engineered streptococcus canis Cas9 variants on single-base PAM targets

ACas9 (ScCas9) ortholog and its engineered variants, possessing novel PAM specificity, is an addition to the family of CRISPR-Cas9 systems. ScCas9 endonuclease is used in complex with guide RNA, consisting of identical non-target-specific sequence to that of the guide RNA SpCas9, for specific recognition and activity on a DNA target immediately upstream of either an 'NNGT' or “NNNGT” PAM sequence. A novel DNA-interacting loop domain within ScCas9, and other Cas9 orthologs, such as those fromandfacilitates a divergent PAM sequence from the “NGG” PAM of SpCas9.

Cas9 as a genome engineering platform with novel PAM specificity

Methods and apparatus relate to the synthesis of polynucleotides having a predefined sequence on a support. Assembly methods include primer extension to generate overlapping construction oligonucleotides and assembly of the polynucleotides of interest onto an anchor support-bound oligonucleotides. Methods and apparatus for selection of polynucleotides having the predefined sequence and/or length are disclosed.

Methods and devices for nucleic acids synthesis

Aspects of the invention relate to methods, compositions and algorithms for designing and producing a target nucleic acid. The method can include: (1) providing a plurality of blunt-end double-stranded nucleic acid fragments having a restriction enzyme recognition sequence at both ends thereof; (2) producing via enzymatic digestion a plurality of cohesive-end double-stranded nucleic acid fragments each having two different and non-complementary overhangs; (3) ligating the plurality of cohesive-end double-stranded nucleic acid fragments with a ligase; and (4) forming a linear arrangement of the plurality of cohesive-end double-stranded nucleic acid fragments, wherein the unique arrangement comprises the target nucleic acid. In certain embodiments, the plurality of blunt-end double-stranded nucleic acid fragments can be provided by: releasing a plurality of oligonucleotides synthesized on a solid support; and synthesizing complementary strands of the plurality of oligonucleotides using a polymerase based reaction.

Compositions and methods for high fidelity assembly of nucleic acids

EngineeredCas9 (ScCas9) variants include an ScCas9 protein with its PID being the PID amino acid composition ofCas9 (SpCas9)-NG, an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 in its amino acid sequence (Sc+), and an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 and a substitution of residues ADKKLRKRSGKLATE [SEQ ID No. 4] in position 365-379 in the ScCas9 open reading frame (Sc++). Also included are CRISPR-associated DNA endonucleases with a PAM specificity of 5'-NG-3&#x2032; or 5&#x2032;-NNG-3&#x2032; and a method of altering expression of a gene product by utilizing the engineered ScCas9 variants.

Applications of engineeredCas9 variants on single-base PAM targets

The present invention relates to a cell based genomic Recorded Accumulative Memory (geRAM) system (also referred to herein as Genomically Encoded Memory (GEM)) for recoding data (i.e., changes in nucleic acid sequences in cellular DNA in response to physical and/or chemical signal(s)) from the cellular environment.

Cell-based genomic recorded accumulative memory

In a method for generating an elongated nucleic acid molecule, a nucleic acid addition of a first nucleic acid molecule attached to a first 3' or 5&#x2032; protecting group to a nucleic acid immobilized on a surface produces an intermediate-length immobilized nucleic acid. The first protecting group is dissociated from the first nucleic acid molecule. A second nucleic acid molecule that is attached to a second associated a 3&#x2032; or 5&#x2032; associated protecting group is added to the intermediate-length nucleic acid. The second associated protecting group is dissociated from the second nucleic acid molecule. A sequentially-extended elongated immobilized nucleic acid molecule having a desired sequence and length is produced by sequentially extending the intermediate-length immobilized nucleic acid by adding additional nucleic acid molecules with associated protecting groups to the intermediate-length nucleic acid and dissociating the associated protecting group after each addition.

Methods for high fidelity production of long nucleic acid molecules

Aspects of the invention relate to methods, compositions for designing and producing a target nucleic acid. In particular, aspects of the invention relate to the multiplex synthesis of target polynucleotides.

Compositions and methods for multiplex nucleic acids synthesis

Methods and apparatus relate to the synthesis of high fidelity polynucleotides and to the reduction of sequence errors generated during synthesis of nucleic acids on a solid support. Specifically, design of support-bound template oligonucleotides is disclosed. Assembly methods include cycles of annealing, stringent wash and extension of polynucleotides comprising a sequence region complementary to immobilized template oligonucleotides. The error free synthetic nucleic acids generated therefrom can be used for a variety of applications, including synthesis of biofuels and value-added pharmaceutical products.

Assembly of high fidelity polynucleotides

Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.

Methods and devices for high fidelity polynucleotide synthesis

Methods and devices are provided for preparing a protein array having a plurality of proteins. In one embodiment, the method includes providing a plurality of nucleic acids each having a predefined sequence and expressing in vitro a plurality of proteins from the plurality of nucleic acids. In another embodiment, protein arrays having a solid surface and a microvolume are also provided. The solid surface can have a plurality of anchor oligonucleotides capable of hybridizing with a plurality of nucleic acids. The microvolume can cover each of the plurality of anchor oligonucleotides and can be configured to produce a polypeptide from each of the plurality of nucleic acids.

Protein arrays and methods of using and making the same

The invention provides compositions and methods for repeatable directed endonucleases (RDEs) and methods for repeatedly, and specifically cleaving DNA offset from the RDE's DNA recognition sequence on the target nucleic acid rather than within the DNA recognition sequence. Conservation of the recognition sequence of the target nucleic acid enables for re-localization of an RDE back to the DNA recognition sequence for further cleavage. The RDEs and methods of the invention are useful in applications including, but not limited to, recording data into a genome, timing the order of biochemical pathway events, efficient genome engineering and encoding lagged cellular death.

Directed endonucleases for repeatable nucleic acid cleavage

Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.

Methods for sorting nucleic acids and multiplexed preparative in vitro cloning

Growing community of inventors

Newton, MA, United States of America

Joseph M Jacobson