Controlling DNA-RNA strand displacement kinetics with base distribution

DNA-RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting DNA-RNA strand displacement reactions is necessary to enable control of processes such as CRISPR-Cas9 gene editing. By combining multi-scale modelling with strand displacement experiments we show that the distribution of bases along the displacement domain of an invading strand has a very strong effect on reaction kinetics. Merely by redistributing bases within a displacement domain of fixed base composition, we are able to design sequences whose reaction rates span more than two orders of magnitude. We characterize this effect in reactions involving the invasion of dsDNA by an RNA strand and invasion of a hybrid duplex by a DNA strand. We show that oxNA, a recently introduced coarse-grained model of DNA-RNA hybrids, can reproduce trends in experimentally observed reaction rates. We also develop a kinetic model for predicting strand displacement rates. On the basis of these results, we argue that base distribution effects are likely to play an important role in the function of the guide RNAs that direct CRISPR-Cas systems.