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.

Azobenzene covalently attached to RNA undergoes trans-to-cis photo-switching on a time scale of ∼15 picoseconds – 30 times slower than in vacuo.

Ultrafast UV/Vis pump/probe experiments on ortho-, meta- and para-hydroxy-substituted azobenzenes (HO-ABs), as well as for sulfasalazine, an AB-based drug, were performed in aqueous solution. For meta-HO-AB, AB-like isomerisation behaviour can be observed, whereas, for ortho-HO-AB, fast proton transfer occurs, resulting in an excited keto species. For para-HO-AB, considerable keto/enol tautomerism proceeds in the ground state, so after excitation the trans-keto species isomerises into the cis form. Aided by TD-DFT calculations, insight is provided into different deactivation pathways for HO-AB, and reveals the role of hydroxy groups in the photochemistry of ABs, as well as their acetylation regarding sulfasalazine. Hydroxy groups are position-specific substituents for AB, which allow tuning of the timescale of thermal relaxation, as well as the amount and contribution of the keto species to photochemical processes.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a beta-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a beta-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.