MOLECULAR-DYNAMICS OF RNA WITH THE OPLS FORCE-FIELD - AQUEOUS SIMULATION OF A HAIRPIN CONTAINING A TETRANUCLEOTIDE LOOP

The results are reported for a 200 ps, unconstrained simulation of the RNA hairpin molecule GGGCGCAAGCCU in aqueous solution with charge-neutralizing counterions. The OPLS force field is used to compute the RNA energies and forces. Periodic, truncated-octahedral boundary conditions coupled with Ewald summations for computing long-range electrostatic interactions are employed. The accuracy of the computational methodology is assessed by a detailed comparison of the structural features derived from the simulation to those obtained from NMR data. The analysis of the simulation shows overall good agreement with experiment, including NMR-derived interproton distances and ribose-phosphate backbone torsion angles. The secondary and overall three-dimensional structure is well preserved throughout die 200 ps trajectory. An interesting structural feature seen in the simulation is the formation of a water-mediated hydrogen bond between the unusual G-A base pair in the loop. Such an interaction may add to the observed stability of this hairpin molecule. Analysis of the cross-correlation of atomic displacements indicates that the loop and stem behave dynamically as distinct structural units.