Molecular Dynamics Study of the Controlled Destabilization of an RNA Hairpin Structure by a Covalently Attached Azobenzene Switch

As shown in recent experimental studies, photoswitches like azobenzene can act as efficient regulators of the folding and unfolding of DNA and RNA duplexes. Here we explore the details of the conformational changes induced by azobenzene attachment, focusing upon a small 14-mer RNA hairpin structure. The azobenzene chromophore is covalently bound to the stem region adjacent to a UUCG tetraloop which is known to represent a particularly stable structure. Since the characteristic time scale of conformational changes exceeds the nanosecond scale (and by far exceeds the ultrafast time scale of trans-to-cis photoswitching), equilibrium simulations using enhanced sampling by replica exchange molecular dynamics (REMD) are employed to investigate the influence of trans versus cis azobenzene attachment on the stability of the hairpin. We report on the analysis of fluctuations and conformational landscapes, along with calculations of relative melting temperatures. The simulations are found to reproduce certain experimentally predicted trends for azobenzene-modified RNA; in particular, both trans and cis conformers have a destabilizing effect. This effect is significantly enhanced for the cis conformer, even though the latter tends to flip out of the double-stranded stem region.