  RNA interference, particularly siRNA induced gene silencing is becoming an
important avenue of modern therapeutics. The siRNA is delivered to the cells as
short double helical RNA which becomes single stranded for forming the RISC
complex. Significant experimental evidence is available for most of the steps
except the process of the separation of the two strands. We have attempted to
understand the pathway for double stranded siRNA (dsRNA) to single stranded
(ssRNA) molecules using steered molecular dynamics simulations. As the process
is completely unexplored we have applied force from all possible directions
restraining all possible residues to convert dsRNA to ssRNA. We found pulling
one strand along helical axis direction restraining far end of the other strand
demands excessive force for ssRNA formation. Pulling a central residue of one
strand, in a direction perpendicular to the helix axis, while keeping the base
paired residue fixed requires intermediate force for strand separation.
Moreover we found that in this process the force requirement is quite high for
the first bubble formation (nucleation energy) and the bubble propagation
energies are quite small. We hypothesize this could be the mode of action
adopted by the proteins in the cells.
