  The forming and melting of complementary base pairs in RNA duplexes are
conformational transitions required to accomplish a plethora of biological
functions. Yet the dynamic steps of these transitions have not been
quantitatively characterized at the molecular level. In this work, the base
opening process was first enforced by atomistic pulling simulations and then
analyzed with a novel reweighting scheme which allowed the free-energy profile
along any suitable reaction coordinate, e.g. solvation, to be reconstructed.
The systematic application of such approach to different base-pair combinations
provides a molecular motion picture of helix opening which is validated by
comparison with an extensive set of experimental observations and links them to
the enzyme-dependent unwinding mechanism. The RNA intrinsic dynamics disclosed
in this work could rationalize the directionality observed in RNA-processing
molecular machineries.
