NMR spectroscopic characterization of the adenine-dependent hairpin ribozyme

Time-resolved NMR spectroscopy was applied to study ribozyme-mediated RNA catalysis in a mutant of the hairpin ribozyme, the adenine-dependent hairpin ribozyme (ADHR; M. Meli, et al. J. Biol. Chem. 2003, 278, 9835-9842) with atomic resolution. The mutant ADHR was designed to investigate the role of cofactors in RNA catalytic mechanisms in order to understand cellular processes that could have been present in the archaic "RNA world" and of their evolution towards functional RNAs in modern cellular processes, as for example, found in the glmS ribozyme. Conformational changes due to RNA cleavage were analyzed following spectral changes of the NMR imino proton resonances that could be assigned both for the pre- and postcleaved conformation for this 80-nucleotide long RNA. (31)P NMR spectroscopic studies allowed us to confirm the formation of a cyclic phosphodiester as a result of the cleavage process. For ADHR, both metal ions and the cofactor adenine are essential for self-cleaving activity. The interaction of the ribozyme with the cofactor adenine is found to be transient and too weak to significantly change the RNA structure or to modulate the spectroscopic characteristics of the cofactor. ADHR therefore represents a ribozyme in which high activation barriers have to be overcome to populate cleavage-competent states that exhibit short life times. We show that conformational dynamics, but not the chemistry, constitute the rate-limiting step in catalysis of the adenine-dependent hairpin ribozyme.