High-fidelity CRISPR genome editing of single-nucleotide mutation with near-complementary guide RNA via enhanced target binding kinetics

The CRISPR-Cas9 system is a powerful genome editing tool capable of precisely recognizing and cleaving specific DNA sequences, and has been extensively investigated as a strategy for correcting mutations associated with genetic diseases and cancer. However, when single-nucleotide mutations do not occur within or near the protospacer adjacent motif (PAM) sequence, conventional CRISPR designs often fail to discriminate between mutant and wild-type alleles. To address this limitation, we developed a guide RNA (gRNA) engineering approach that introduces an intentional mismatch within the seed region of the gRNA. These near-complementary gRNAs retain strong binding affinity to the mutant sequence while significantly reducing affinity for the wild-type, thereby enabling highly specific genome editing of single-base mutations without reliance on PAM proximity. As a proof of concept, we applied this strategy to the clinically relevant G228A (-124C > T) mutation in the TERT promoter, a cancer-specific single-nucleotide mutation frequently found in glioblastomas and other tumors, that does not generate a canonical PAM sequence. Our near-complementary gRNA successfully induced selective editing of the mutant allele while sparing the wild-type sequence. Furthermore, single-molecule fluorescence resonance energy transfer (smFRET) analysis revealed distinct differences in binding kinetics between mutant and wild-type DNA, providing kinetic insight into the discrimination process. In conclusion, this study presents a PAM-independent CRISPR editing strategy for the precise targeting of single-nucleotide mutations and offers a molecular framework for expanding the specificity and applicability of CRISPR-based genome editing technologies.