  In an effort to design efficient platform for siRNA delivery, we combine all
atom classical and quantum simulations to study the binding of small
interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our
results show that siRNA strongly binds to SWCNT surface via unzipping its
base-pairs and the propensity of unzipping increases with the increase in the
diameter of the SWCNTs. The unzipping and subsequent wrapping events are
initiated and driven by van der Waals interactions between the aromatic rings
of siRNA nucleobases and the SWCNT surface. However, MD simulations of double
strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less
unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This
interesting difference is due to smaller interaction energy of thymidine of
dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by
dispersion corrected density functional theory (DFT) methods. After the optimal
binding of siRNA to SWCNT, the complex is very stable which serves as one of
the major mechanisms of siRNA delivery for biomedical applications. Since siRNA
has to undergo unwinding process with the effect of RNA- induced silencing
complex, our proposed delivery mechanism by SWCNT possesses potential
advantages in achieving RNA interference (RNAi).
