Yale University

Agilent Technologies, Inc.

Farren J Isaacs

Miriam Amiram

Jesse Rinehart

Adrian Haimovich

Jeffrey Robert Sampson

Dieter Söll

Jaymin Patel

Natalie Ma

Dieter Soil

Ryan Gallagher

Karl Barber

Alexis Rovner

Colin Hemez

Edward Barbieri

Compositions and methods for gene editing are provided. The methods employ an oligo-based annealing mechanism that is rooted in the process of DNA replication rather than homologous recombination (HR). Oligo incorporation efficiencies are comparable and often exceed those of CRISPR/cas9 editing without the need for double strand breaks (DSBs). By relying on the multiplex annealing of oligos rather than DSBs the process is highly scalable across a genomic region of interest and can generate many scarless modifications of a chromosome simultaneously. Combinatorial genomic diversity can be generated across a population of cells in a single transformation event; genomic landscapes can be traversed through successive iterations of the process, and genome-wide changes can be massively parallelized and amplified through systematic strain mating.

Multiplex genome engineering in eukaryotes

The present invention relates to libraries of phosphopeptide-encoding oligonucleotides and methods of preparing such libraries. The present invention also relates to methods of detecting, visualizing, or screening for phosphorylation-dependent protein-protein interactions using recombinant phosphopeptides and/or phosphopeptide-encoding oligonucleotides. The present invention also relates to sets or kits of oligonucleotides having regions that encode phosphopeptides.

Phosphopeptide-encoding oligonucleotide libraries and methods for detecting phosphorylation-dependent molecular interactions

Compositions, systems, and methods for preparation of polypeptides having multiple iterations of non-standard amino acids are provided. The compositions and method can be used to produce recombinant proteins at a greater yield than the same or similar polypeptides made using conventional compositions, systems, and methods. Accordingly, in some embodiments, the polypeptides are ones that could not be made using conventional methods and reagents, or could not be made a sufficient yield or purity to serve a practical purpose using conventional methods and reagents. Polypeptides made using the disclosed compositions, systems, and methods are also provided.

Compositions and methods of use thereof for making polypeptides with many instances of nonstandard amino acids

Methods and strategies for introducing genetic safeguards into microorganisms, genetically modified organisms (GMO) including the safeguards, and methods of use thereof are provided. The genetic safeguards generally impart a low escape frequency, are robust, and are modular. Safeguards with low escape frequency prevent the rise of mutants escaping defined media and limit growth in the wild. Robust safeguards retain wild-type levels of fitness while also maintaining containment in diverse growth conditions.

Compositions and methods for biocontainment of microorganisms

Organisms resistant to horizontal gene transfer (HGT), and compositions and methods of use thereof are provided. The organisms are typically genomically recoded organisms (GRO), typically cells, having a genome in which at least one endogenous codon has been eliminated by reassignment of the codon to a synonymous or non-synonymous codon. The GRO typically include a recombinant expression construct for expression of at least one element of a ribosomal rescue pathway, typically lacking the eliminated codon. Typically, the disclosed cells are resistant to completed transfer and/or expression of a horizontally transferred genetic element (HTGE) from another organism compared a corresponding cell having a genome wherein the eliminated codon has not been eliminated. In some embodiments, the organism from which the HTGE is being transferred is a bacterium or a virus.

Engineering organisms resistant to viruses and horizontally transferred genetic elements

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Stamford, CT, United States of America

Farren J Isaacs