In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers.

摘要: The design of optimal photoswitches to regulate nucleic acid functionality is a considerable challenge. Azobenzene switches that are covalently bound the backbone paradigm example has been studied using different types linker species connecting chromophore backbone. To support experimental efforts construct azobenzene–linker–RNA combinations, we introduce here systematic approach for theoretical analysis, which provides criteria local embedding via chosen linker. Using reference frame adapted chromophore, quantitative measures provided (i) propensity stacking in competition with drift toward minor or major groove, (ii) tendency disrupt native hydrogen bond network, (iii) structural flexibility chromophore–linker combination, and (iv) correlations presence base opposite strand. Large differences stability between trans ci...