Remarkable similarity of force induced dsRNA conformational changes to stretched dsDNA and their detection using electrical measurements

Abstract

In spite of the striking difference between twist-stretch coupling of dsRNA and dsDNA under external force, dsRNA shows similar structural polymorphism to dsDNA under different pulling protocols. Our atomistic MD simulations show that overstretching dsRNA along the 3′ direction of the opposite strands (OS3) leads to the emergence of S-RNA whereas overstretching along the 5′ directions of the opposite strands (OS5) leads to melting of dsRNA at lower forces. Using the dsRNA morphology from pulling MD simulations, we use a multiscale method involving ab initio calculations and Kinetic Monte Carlo (KMC) simulations to estimate the conductance of dsRNA and find that the conformational changes drastically affect its conductance. The current through dsRNA chains drastically drops after a critical stretching length and critically depends on the pulling protocol. The critical stretching length for the OS3 pulling case is around 65% higher than that of the OS5 case.