DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway

A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). In vitro biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of E. coli with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the APPlon mutation in Alzheimer’s disease without disrupting the APPwt locus. It is worth mentioning that the APPlon sequence has only one base difference from that of APPwt. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.