Complex Formations between Artificial RNA-DNA Chimera Nucleic Acids and RNA Modification Enzyme

In living cells, RNA modification enzymes form multiple styles of RNA-protein complexes with various precursor RNA species for generation of mature RNA molecules. In general, however, preparation of the processing-modification complex is very difficult, because the complex is dissociated according to progress of the enzymatic reactions. Until now, several ways to prevent the dissociation of complexes have been devised, for examples utilization of small substrate analogues and/or disruption of the catalytic center of the enzyme. However, in the case of some RNA methyltransferases such as tRNA (Gml8) methyltransferase [TrmH], these approaches are not successful. TrmH enhances the affinity for RNA only in the presence of the methyl group donor, S-adenosyl-L-methionine (AdoMet). AdoMet analogues do not work like AdoMet in the case of TrmH, because TrmH requires the activated methyl group in AdoMet for structural change of the enzyme. Furthermore, disruptions of the catalytic center (Arg41 residue) by amino acid substitutions cause perturbation of the local protein structure around the catalytic center and result in decrease of the affinity for RNA. Therefore, a new approach for stabilization of the RNA-protein complex is desired. In the current study, we prepared artificial RNA-DNA chimera nucleic acids, in which ribonucleotide(s) is substituted by deoxyribonucleotide(s). Some of the artificial nucleic acids formed stable complexes with TrmH.