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CRISPR-based editing has revolutionized genome engineering despite the observation that many DNA sequences remain challenging to target. Unproductive interactions formed between the single guide RNA's (sgRNA) Cas9-binding scaffold domain and DNA-binding antisense domain are often responsible for such limited editing resolution. To bypass this limitation, we develop a functional SELEX (systematic evolution of ligands by exponential enrichment) approach, termed BLADE (binding and ligand activated directed evolution), to identify numerous, diverse sgRNA variants that bind Streptococcus pyogenes Cas9 and support DNA cleavage. These variants demonstrate surprising malleability in sgRNA sequence. We also observe that particular variants partner more effectively with specific DNA-binding antisense domains, yielding combinations with enhanced editing efficiencies at various target sites. Using molecular evolution, CRISPR-based systems could be created to efficiently edit even challenging DNA sequences making the genome more tractable to engineering. This selection approach will be valuable for generating sgRNAs with a range of useful activities. [Display omitted] • In vitro evolution generates multiple functional gRNA scaffolds • sgRNAs are highly malleable • sgRNA scaffold variants display varied efficacy with different sgRNA spacer domains • Functional sgRNA selection can generate novel sgRNAs with useful properties Bush et al. present a high-throughput selection and RNA evolution scheme that can identify functional sgRNA scaffold domains with distinct properties. These variants provide additional insight into the structure-activity-relationships required for effective Cas9 guided DNA editing. BLADE SELEX promises to facilitate the development of sgRNA variants with new activities. [ABSTRACT FROM AUTHOR]