Prime editing guide RNA (pegRNA) core scaffold (pegRNA scaffold)

The Prime editing guide RNA (pegRNA) core scaffold is a critical structural component of the prime editing system, a versatile search-and-replace genome editing technology [1]. It consists of the conserved RNA sequence that facilitates the binding of the guide RNA to the Cas9 nickase-reverse transcriptase (RT) fusion protein [1]. Unlike standard single-guide RNAs (sgRNAs), the pegRNA includes a 3' extension containing a primer binding site (PBS) and a reverse transcriptase template (RTT), but the core scaffold remains the essential link between the targeting spacer and the enzymatic machinery [2]. By stabilizing the ribonucleoprotein complex, the scaffold ensures that the Prime Editor is accurately positioned at the genomic target site [3]. This molecular architecture allows for precise nucleotide substitutions, insertions, and deletions without requiring double-strand breaks or exogenous donor DNA [1]. While not a therapeutic target in the traditional sense, the pegRNA scaffold is a primary focus of engineering to improve editing efficiency and stability in treating genetic disorders [2]. Optimization of the scaffold, such as the addition of structured RNA motifs like evopreQ1, has been shown to enhance the performance of prime editing across various cell types [2]. These advancements are crucial for the clinical translation of prime editing to treat diseases like sickle cell anemia and cystic fibrosis [3].

Other names

pegRNA constant regionCRISPR-Cas9 guide RNA scaffoldsgRNA scaffold (prime editing)

The scaffold sequence forms specific secondary structures (hairpins) that are recognized and bound by the Cas9 protein, thereby tethering the targeting spacer and the 3' reverse transcription template to the genomic locus [1][2].