gRNAn

gRNAn is a notational term used in some discussions to denote a guide RNA of length n in CRISPR genome editing systems. It is not a distinct molecular class, but a way to refer to the spacer portion of a guide RNA when considering different lengths. In common practice, guide RNAs direct a Cas nuclease to a complementary DNA sequence, and the term can be applied across various Cas proteins that use RNA-guided targeting.

A typical functional gRNA consists of a spacer sequence of length n that binds the target and a scaffold region that interacts with the Cas protein. In many widely used systems such as SpCas9, the spacer is around 20 nucleotides, but researchers have explored shorter or longer spacers to study effects on activity and specificity. Thus, gRNAn denotes a guide RNA with a spacer of length n, while leaving the scaffold and backbone constant or adapting them as needed for a given Cas variant.

Design considerations for gRNAn include choosing a target adjacent to a suitable protospacer adjacent motif (PAM) compatible with the Cas nuclease, balancing GC content, minimizing predicted off-target interactions, and avoiding strong secondary structures that could impede binding. Chemical modifications and delivery methods may also influence stability and performance of gRNAn in cells.

Applications of gRNAn concepts encompass gene knockout, gene knock-in, transcriptional regulation with CRISPR interference or activation, and advanced approaches like base editing or prime editing. While the general idea of gRNA length is widely studied, the explicit term gRNAn is largely a descriptive convenience rather than a standardized specification in most protocols.