C2 - UV surface-enhanced resonance Raman (SERR) spectro-electrochemistry for elucidating structure, dynamics, and function of nucleic acid complexes

The function of RNA and DNA molecules often requires dynamic interaction with other nucleic acids (NAs) or proteins. Techniques that provide atomic-scale structural information under close-to-physiological conditions are required to unravel the molecular mechanism of such interactions. The focus of this project is to introduce a new experimental platform, namely surface-enhanced spectroscopy combined with UV Resonance Raman (UV SERR), and to apply this technique to two enzymatic activities of molecules provided by B1 and B3. The novelty of the UV SERR technique lies in the molecule-selective and amplified detection to monitor the vibrational signature of NAs (or proteins) interfaced as monolayers on a metal support. The method can resolve the dynamics of structural changes from milliseconds to minutes. Additionally, the SERR method can be combined with electrochemical experiments: the metal support can serve as a reaction partner to control redox reactions by voltage. We will apply this method to unravel the local and global spatiotemporal organization of NA-NA and NA-protein complexes. One model is the DNAzyme 10-23 (B3), which catalytically cleaves the target RNA, and its activity is modulated by cations. We will explore the interaction between DNAzyme 10-23 and its target RNA during catalysis in real-time on a millisecond-to-second timescale. The second system is RNA-binding photoreceptor PAS-ANTAR-LOV (PAL) harbouring a redox-active FMN chromophore as an active site (B1, B2). We will explore if PAL’s activity can be regulated electrochemically and what structural changes are induced by a voltage step.