Maturation of siRNA by strand separation: Steered molecular dynamics study

Abstract

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 the helical axis direction restraining the 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 believe the success rate of the design of siRNA sequences for gene silencing may increase if this mechanistic knowledge is utilized for such a design process.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular dynamics
• force induced rupture and unzipping
• stacking parameters

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

We gratefully acknowledge SERB and DST, New Delhi, India, for their financial support through project numbers PDF/2015/000308, and PDF/2017/002110/CS. RKM also thank UGC for D. S. Kothari fellowship with the award number F4-2/2006(BSR)/PHY/18-19/0060. This work was supported by University Grants Commission, India and Science and Engineering Research Board.