Abstract: Described in several example embodiments herein are engineered programmable pattern recognition compositions and uses thereof. In an embodiment, the engineered protein contains an NTPase of a Signal Transduction ATPases with Numerous-associated Domains (STAND) superfamily (STAND NTPase), comprising a pathogen-associated molecular pattern (PAMP) recognition activity, wherein the STAND NTPase and the PAMP recognition activity are derived from the same or different prokaryotes.

Abstract: Described in certain example embodiments herein are programmable nuclease-peptidase compositions, systems, and methods for the manipulation of nucleic acids and/or polypeptides. In some embodiments, the programmable nuclease-peptidase composition comprises a repeat-associated mysterious protein (RAMP) polypeptide; a guide molecule capable of forming a RAMP-guide molecule complex with the RAMP polypeptide and directing sequence specific binding of the complex to a target polynucleotide; and a peptidase capable of binding to the RAMP polypeptide, the guide molecule, or further complexing with the RAMP-guide molecule complex, wherein binding of the RAMP-guide molecule complex to the target polynucleotide initiates binding and/or interaction of the peptidase with a target polypeptide.

Abstract: Described in certain example embodiments herein are programmable nuclease-peptidase compositions, systems, and methods for the manipulation of nucleic acids and/or polypeptides. In some embodiments, the programmable nuclease-peptidase composition comprises a repeat-associated mysterious protein (RAMP) polypeptide; a guide molecule capable of forming a RAMP-guide molecule complex with the RAMP polypeptide and directing sequence specific binding of the complex to a target polynucleotide; and a peptidase capable of binding to the RAMP polypeptide, the guide molecule, or further complexing with the RAMP-guide molecule complex, wherein binding of the RAMP-guide molecule complex to the target polynucleotide initiates binding and/or interaction of the peptidase with a target polypeptide.

Abstract: Engineered or non-naturally occurring systems and compositions comprising novel Type V Cas polypeptides and orthologs thereof are disclosed herein. Also provided are methods of use for the novel Type V Cas polypeptide systems and compositions for reprogrammable targeting of nucleic acid and polynucleotide components.

Abstract: The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, nucleic acid editing. Novel nucleic acid targeting systems comprise components of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements. Specifically, the disclosure provides an engineered composition comprising: a programmable DNA-binding protein and two or more Tn7-like transposition proteins, wherein at least one of the Tn7-like transposition proteins is connected to the DNA-binding protein or otherwise capable of forming a complex with the DNA-binding protein, wherein the DNA-binding protein comprising a Cas protein including a Cas12k protein, and wherein two or more Tn7-like transposition proteins consisting of TnsB, TnsC, and TniQ.

Abstract: The invention provides for systems, methods, and compositions for targeting and editing nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a DNA-targeting Cpf1 protein, at least one guide molecule, and at least one adenosine deaminase protein or catalytic domain thereof.

Abstract: The invention provides for systems, methods, and compositions for targeting and editing nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a DNA-targeting Cpf1 protein, at least one guide molecule, and at least one adenosine deaminase protein or catalytic domain thereof.

Abstract: Systems and methods for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. The novel nucleic acid targeting systems can comprise components of one or more transposases, one or more components of a CRISPR-Cas system, and a transposable element.

Abstract: Compositions, systems and methods for targeted gene modification, insertion and perturbation of gene transcripts and nucleic acid editing are provided. In particular, helitron-mediated gene targeting systems and methods of their use are detailed and provided herein.

Abstract: The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, nucleic acid editing. Novel nucleic acid targeting systems comprise components of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements.

Abstract: Embodiments herein include engineered CRISPR-Cas effector proteins that comprise at least one modification compared to an unmodified CRISPR-Cas effector protein (e.g., C2c1) that enhances binding of the of the CRISPR complex to the binding site and/ or alters editing preference as compared to wild type. Embodiments disclosed further include viral vectors for delivery of CRISPR-Cas effector proteins. The vectors may be designed to allow packaging of the CRISPR-Cas effector protein within a single vector. Certain embodiments further include delivery vectors, constructs, and methods of delivering larger genes for systemic delivery.

Abstract: The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, nucleic acid editing. Novel nucleic acid targeting systems comprise components of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements.

Abstract: Systems and methods for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. Novel nucleic acid targeting systems comprise components of CRISPR systems, reverse transcriptase, pegRNAs, paired pegRNAs or modified pegRNAs, DNA processing proteins, recombinases, proteins for inhibiting nucleases, and proteins for promoting ssDNA annealing.

Abstract: The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, nucleic acid editing. Novel nucleic acid targeting systems comprise components of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements.

Abstract: The disclosure provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered RNA-targeting systems comprising a novel RNA-targeting Cas12b effector protein and at least one targeting nucleic acid component like a guide RNA or crRNA.

Abstract: Embodiments herein include engineered CRISPR-Cas effector proteins that comprise at least one modification compared to an unmodified CRISPR-Cas effector protein that enhances binding of the CRISPR complex to the binding site and/or alters editing preference as compared to wild type. In certain embodiments, the CRISPR-Cas effector protein is a Type V-B effector protein, e.g., C2c1. Embodiments also include viral vectors for delivery of CRISPR-Cas effector proteins, including C2c1. In certain embodiments, the vectors allow packaging of the CRISPR-Cas effector protein within a single vector. The disclosure also includes delivery vectors, constructs, and methods of delivering larger genes for systemic delivery.

Abstract: The invention provides for systems, methods, and compositions for targeting and editing nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a DNA-targeting Cpf1 protein, at least one guide molecule, and at least one adenosine deaminase protein or catalytic domain thereof.

Abstract: The present application provides systems, methods and compositions used for targeted gene modification, targeted insertion, perturbation of gene transcripts, nucleic acid editing. Novel nucleic acid targeting systems comprise components of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems and transposable elements.