Mesoscopic Calculation of Single Mismatches in RNA/DNA Hybrids: Strong Hydrogen Bonds of dTrG Affect CRISPR...

In nature, complementary DNA-RNA hybrids occur in several biological contexts, mainly related to transcription, replication, and gene regulation. Despite their importance, mismatches in DNA-RNA hybrids are not as well characterized as in the case of DNA-DNA or RNA-RNA pairing. Of particular concern are strong mismatches between DNA and RNA strands that may favor off-target binding in CRISPR-Cas gene editing. Here, we investigate the effect of single internal mismatches on the thermal stability of RNA/DNA sequences using a mesoscopic approach based on published melting temperatures, as well as new measurements, to estimate hydrogen bonds and stacking interaction potentials. Our results show that only dTrG base pairs have substantial hydrogen bonding, even larger than the Watson-Crick dTrA pair, while all others are negligible. However, we show that in many cases stacking provides some stability to the otherwise weaker mismatches. Our results provide an explanation for the stability of dTrG as well as why it has CRISPR editing efficiencies similar to those of perfect matches.