Unraveling siRNA Unzipping Kinetics with Graphene

TL;DR

This study uses molecular dynamics simulations to explore how siRNA unzips and binds spontaneously to graphene, revealing faster unzipping at higher temperatures and stronger interactions compared to DNA.

Contribution

It provides detailed insights into the unzipping kinetics and interaction strengths of siRNA with graphene, highlighting the spontaneous unzipping process and energy barriers involved.

Findings

siRNA unzips spontaneously on graphene within nanoseconds

Unzipping initiates at one end and propagates, with the middle remaining double stranded

Unzipping time decreases exponentially with temperature

Abstract

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (t) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.