Abstract: Compositions and methods for isolating new variants of known clustered regularly-interspaced short palindromic repeat (CRISPR) RNA-guided nuclease (RGN) genes and new CRISPR systems are provided. The methods find use in identifying CRISPR RGN gene variants in complex mixtures. Compositions comprise hybridization baits that hybridize to CRISPR RGN genes of interest in order to selectively enrich variant polynucleotides from complex mixtures. Bait sequences may be specific for a number of CRISPR RGN genes from distinct gene families of interest and may be designed to cover each CRISPR RGN gene of interest by at least 2-fold. Bait pools may also comprise baits for sequences flanking CRISPR RGN genes of interest to allow for the identification of tracrRNAs corresponding to novel CRISPR RGN variants and a complete CRISPR system comprising a CRISPR RGN and its associated guide RNA.

Abstract: Compositions and methods for binding to a target sequence of interest are provided. The compositions find use in cleaving or modifying a target sequence of interest, visualization of a target sequence of interest, and modifying the expression of a sequence of interest. Compositions comprise RNA-guided nuclease polypeptides, CRISPR RNAs, trans-activating CRISPR RNAs, guide RNAs, and nucleic acid molecules encoding the same. Vectors and host cells comprising the nucleic acid molecules are also provided. Further provided are CRISPR systems for binding a target sequence of interest, wherein the CRISPR system comprises an RNA-guided nuclease polypeptide and one or more guide RNAs.