Structure and dynamics of adenosine loops in RNA bulge duplexes. RNA hydration at the bulge site

An RNA bulge duplex resulted from annealing of oligoribonucleotides: GUCGAAPAGCUG and CAGCCGAC, where 2-aminopurine (AP) was introduced as a fluorescent conformational probe, has been studied by in aqua molecular dynamics simulation (AMBER force field, 250 ps at 300 K, cutoff 15 Angstrom; Cray J916) to complement our results of laser spectrofluorimetry measurements of the same duplex. During the entire MD run, the stem regions maintained their conformational stability. The RNA molecule showed a considerable axis bending. The hydrogen bonds and stacking interactions within the molecule were preserved and sugar puckering remained typical for A-RNA. On the other hand, the bulged nucleotide residues showed a tendency to "bulge out" to the exterior which resulted in destabilisation of their closest neighbourhood, which was clearly indicated by the conformational parameters of the stem/bulge contact region. The hydration pattern observed at the bulge site clearly suggests that this part of RNA is specifically stabilised by water hydrogen bonding network. In addition, the 2-aminopurine residue forms C-H ... O hydrogen bonds with water molecules. Dynamics of individual water molecules surrounding the bulge loop region of the RNA duplex has been analysed. The map of hydration network strongly indicates that water has to be treated as an integral part of the RNA structure.