Zymergen Inc.

Harvard College

Brian Chaikind

Kenneth S Bruno

Sean Poust

Sara Da Luz Areosa Cleto

Patrick J Westfall

Arthur Muir Fong, Iii

Edyta Szewczyk

Vytas SunSpiral

Hassan Abdulla

Jennifer Fredlund

Paolo Boccazzi

Dylan Vaughan

Kyle Rothschild-Mancinelli

David R Liu

Shawn Szyjka

Kedar Patel

Aaron Miller

Jeffrey L Bessen

Hendrik M Van Rossum

Paul Perkovich

Hendrik Marinus Van Rossum

Some aspects of this disclosure provide a fusion protein comprising a guide nucleotide sequence-programmable DNA binding protein domain (e.g., a nuclease-inactive variant of Cas9 such as dCas9), an optional linker, and a recombinase catalytic domain (e.g., a tyrosine recombinase catalytic domain or a serine recombinase catalytic domain such as a Gin recombinase catalytic domain). This fusion protein can recombine DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. The instant disclosure represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state.

Programmable CAS9-recombinase fusion proteins and uses thereof

A HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols is provided. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods for isolating clonal populations derived from individual fungal spores are also provided.

HTP genomic engineering platform for improving fungal strains

HTP genomic engineering platform for improving filamentous fungal cells that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. Methods can be carried out within optofluidic devices.

Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations. High throughput methods of CRISPRi and CRISPRa.

Applications of CRISPRi in high throughput metabolic engineering

Methods, compositions, and kits for high throughput DNA assembly reactions in vitro. Modular CRISPR DNA constructs comprising modular insert DNA parts flanked by cloning tag segments comprising pre-validated CRISPR protospacer/protospacer adjacent motif sequence combinations.

Modular universal plasmid design strategy for the assembly and editing of multiple DNA constructs for multiple hosts

Growing community of inventors

Oakland, CA, United States of America

Brian Chaikind