Unzipping and binding of small interfering RNA with single walled Carbon Nanotube: a platform for small interfering RNA delivery

TL;DR

This study uses classical and quantum simulations to demonstrate that siRNA strongly binds and unzips on single-walled carbon nanotubes, offering a promising platform for RNA delivery in biomedical applications.

Contribution

It reveals the unzipping mechanism of siRNA on SWCNTs and compares it with dsDNA, highlighting the role of van der Waals interactions and nanotube diameter in binding efficiency.

Findings

siRNA strongly binds and unzips on SWCNT surface

Unzipping increases with larger SWCNT diameters

siRNA-SWCNT complex is highly stable

Abstract

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).