CRISPR-based gene-drive system for inhibiting antibiotic resistance of bacteria, including Escherichia coli that efficiently copies a gRNA cassette and adjacent cargo that are flanked with sequences homologous to the targeted gRNA/Cas9 cleavage site. This “pro-active” genetic system (Pro-AG) functionally inactivates an antibiotic resistance marker on a high copy number plasmid with greater efficiency than control CRISPR-based methods. Pro-AG can effectively edit large plasmids or single-copy genomic targets, or introduce functional genes, with numerous applications to biotechnology and biomedicine.

This disclosure provides compositions and methods for altering or changing the tissue tropism, e.g., liver tropism, of adeno-associated viruses (AAV).

Disclosed are cells that have stably integrated into their genomes exogenous nucleic acid sequences, such as transgenes, within or proximal to the integration site of a sequence comprising at least part of an endogenous retrovirus (ERV) or a LTR-retrotransposon (LTR-RT), or instead of a sequence encompassing an ERV or a LTR-RT that is part or was part of the genome of the cell, as well as method of producing and using such cells. Advantageously, a high level and/or stable production of the transgene expression product(s) can be achieved. Transgene integration and expression may be furthered by modulating the DNA repair pathways of the cell, e.g., by transiently expressing a gene encoding a protein that forms part of a DNA repair pathway during transgene integration.

Embodiments of the present disclosure are directed to a method that includes contacting a population of plant cells with a messenger ribonucleic acid (mRNA) construct including a sequence encoding a rare-cutting endonuclease and a detectable label, wherein the rare-cutting endonuclease is configured to induce a mutation at a target genomic locus. The method further includes screening the population of plant cells for the detectable label to identify target plant cells that are genetically transformed with the mRNA construct.

Systems and kits are disclosed herein for genetic engineering (such as for DNA cleavage and gene-editing), which include catalytic nucleic acids and catalytic nucleic acid-assisting reagents. Methods of genetic engineering are also described, in which both catalytic nucleic acid-assisting reagents and catalytic nucleic acids are specific for a target site, thus, providing high-fidelity genetic engineering.

The present disclosure provides for endonuclease enzymes as well as methods of using such enzymes or variants thereof.

The present disclosure relates to systems, compositions and methods for modifying target nucleic acid sequences.

Described is an assay termed Programmable Enzyme-Assisted Selective Exponential Amplification (PASEA) that concurrently amplifies both wild type and mutant alleles while selectively cleaving the former. With time, the rare mutant alleles dominate, and are readily detectable by direct detection, Sanger sequencing, and other readily available methods. Also described are point-of-care assays and microfluidic devices for performing PASEA.

Aspects of this invention inter alia relate to novel systems for targeting, editing or manipulating DNA in a cell, comprising one or more heterologous vector(s) encoding a SluCas9 nuclease from Staphylococcus lugdunensis or variants thereof, and one or more guide RNAs (gRNAs), or a SluCas9 nuclease or variant thereof and one or more gRNAs.

The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.