Analysis. We utilized the last 5 ns of the REMD trajectory at 298 K for the following analysis. Base stacking energies were defined as the electrostatic and van der Waals interaction energies between the adjacent bases. The molecular orientation was expressed by the order parameters S 2 of the C-H bond vectors employing the model-free approach of Lipari and Szabo (51) . After a translational and rotational fit of each RNA snapshot to the ideal A-form helical structure, the order parameters were taken from the plateau phase of the correlation function, given by