2′-<i>O</i>-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR–Cas12a systems
Yuqing Ke, Behafarid Ghalandari, Shiyi Huang, Sijie Li, Chengjie Huang, Xiao Zhi, Daxiang Cui, Xianting Ding
Abstract
-methyl (2'-OMe) modified guide RNA (gRNA) to promote the Cas12a's specificity. Gibbs free energy analysis demonstrates that the 2'-OMe modifications at the 3'-end of gRNA effectively suppress the Cas12a's overall non-specific affinity while maintaining high on-target affinity. For general application illustrations, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms are developed to validate the enhanced Cas12a's specificity. Our results indicate that the 2'-OMe modified gRNAs could discriminate single-base mutations with at least two-fold enhanced specificity compared to unmodified gRNAs. Furthermore, we investigate the enhancing mechanisms of the 2'-OMe modified Cas12a systems by molecular docking simulations and the results suggest that the 2'-OMe modifications at the 3'-end of gRNA reduce the Cas12a's binding activity to off-target DNA. This work offers a versatile and universal gRNA design strategy for highly specific Cas12a system development.