DNAzymes as seen by and with EPR/ESR spectroscopy: structural and functional features

Giuseppe Sicoli, CNRS UMR 8516, Lille University, LASIRE – Laboratory of Advanced Spectroscopy on Interactions, Reactivity and Environment, C4 Building, Avenue Paul Langevin, F–59655 Villeneuve d’Ascq, France, giuseppe.sicoli@univ-lille.fr

Cleavage and ligation of DNAs and/or RNAs can be classified as a vital process in all living systems. For example, topoisomerase enzymes resolve topological problems of DNA in replication, transcription and other cellular transactions by cleaving one or both strands of the DNA; restriction enzymes protect the cell against virus infection by cleavage of the foreign DNA or by degrading cellular DNA during apoptosis of the affected cell. DNAzymes (known also as dexoxyribozymes) have been isolated by in vitro selection; they can be classified as "artificial enzymes". DNAzymes can form duplex and triplex substructures that flank a highly conserved catalytic core. Insights on the structural and mechanistic features of DNAzymes are severely lacking. The role of metal cofactor(s), often paramagnetic species, in such systems has not yet been elucidated. Electron Spin Resonance (also known as Electron Paramagnetic Resonance) is the method of choice for deciphering structural and mechanistic features of the paramagnetic species involved into the chemical reactions. Hyperfine and dipolar spectroscopy have been used for detecting short- and long-range interactions, respectively. The preliminary results obtained on selected cleaving/cleaved architectures pave the way for analysis on mixtures where also metals/lanthanides are used as cofactors, having reached resolution of single nucleotide and beyond. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of spectroscopic studies, both in vitro and in vivo matrices.

In the context of the IBC seminar series

Organised by https://biologischechemie.univie.ac.at/