Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C‐Nucleoside

Abstract

Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C-nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans-to-cis isomerization was investigated by using melting point studies and compared with the known D-threoninol-based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in-vivo and nanoarchitecture photoregulation applications of RNA.

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

“…The conclusion that the βD-Azo/(AP) system exhibits the largest difference in structural stability between trans-and cis-azobenzene-tethered RNA at room temperature is in good agreement with our recent experimental findings. 25 It has been found by Asanuma et al 23 that a more effective photoswitching, entailing a larger difference in melting temperature between the trans and cis forms of RNA hybridization, is feasible for the DT linker without a moiety in the opposite strand but only at elevated temperature. It should also be noted that our previous results for an azobenzene in DNA with the LT linker and without any moiety in the opposite strand showed destabilization of DNA only at elevated temperature.…”

“…In particular, the D-threoninol (DT) and Lthreoninol (LT) linkers have been introduced in refs 26 and 30, and the β-deoxyribose (βD) linker has been addressed in our recent work. 25 Figure 2 illustrates a βD-azobenzene substituted RNA duplex.…”

“…Hence, we use here suitable measures of (de)-stabilization, notably stacking and hydrogen bonding. 24,25,29 Stacking interactions between adjacent bases and Watson− Crick hydrogen bonding between base pairs are the two main factors contributing to the stability of DNA and RNA duplexes. 46,47 Although the relative importance of these two types of interactions is still controversial, stacking interactions are thought to play a predominant role on the grounds of experimental investigations.…”

Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

“…[28] Recent studies have shown that even asmall change of the 2'-substituent of the azobenzene C-nucleosides influences the photo-controlled duplex (de)stabilization of DNA nanoarchitecture. Azobenzene photoswitches have been widely applied for photo-control of nucleic acids due to the different stacking properties of the (E)-and (Z)-azobenzene moiety.Especially, the azobenzene C-nucleosides show excellent photochemical behavior due to their ability to completely isomerize in both isomeric forms (E and Z)i naduplex even at room temperature.…”

Photochromic Materials in Biochemistry

“…In a recent study, the hybridization of RNA was controlled with light by incorporating an azobenzene group into the structure of a ribose unit on the oligonucleotide strand [100]. The nitrogenous base was substituted for an azobenzene derivative (Figure 9.16).…”