Functional dynamics of RNA ribozymes studied by NMR spectroscopy

Abstract

Catalytic RNA motifs (ribozymes) are involved in various cellular processes. Although functional cleavage of the RNA phosphodiester backbone for self-cleaving ribozymes strongly differs with respect to sequence specificity, the structural context, and the underlying mechanism, these ribozyme motifs constitute evolved RNA molecules that carry out identical chemical functionality. Therefore, they represent ideal systems for detailed studies of the underlying structure-function relationship, illustrating the diversity of RNA's functional role in biology. Nuclear magnetic resonance (NMR) spectroscopic methods in solution allow investigation of structure and dynamics of functional RNA motifs at atomic resolution. In addition, characterization of RNA conformational transitions initiated either through addition of specific cofactors, as e.g. ions or small molecules, or by photo-chemical triggering of essential RNA functional groups provides insights into the reaction mechanism. Here, we discuss applications of static and time-resolved NMR spectroscopy connected with the design of suitable NMR probes that have been applied to characterize global and local RNA functional dynamics together with cleavage-induced conformational transitions of two RNA ribozyme motifs: a minimal hammerhead ribozyme and an adenine-dependent hairpin ribozyme. © 2012 Springer Science+Business Media, LLC.