Physical Sciences and Mathematics Commons^™

Non-Watson-Crick Basepairing And Hydration In Rna Motifs: Molecular Dynamics Of 5s Rrna Loop E, Neocles B. Leontis, Kamila Réblová, Nad'a Špačková, Richard Štefl, Kristina Csaszar, Jaroslav Koča, J Sponer

Chemistry Faculty Publications

Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of > 80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg2+ rigidifies Loop E and stabilizes its major groove at an intermediate …