Unzipping of Double-Stranded Ribonucleic Acids by Graphene and Single-Walled Carbon Nanotube: Helix Geometry versus Surface Curvature

Using atomistic molecular dynamics simulations, we report graphene-assisted spontaneous unzipping of a novel duplex ribonucleic acid analogue xylonucleic acid (XNA) at physiologically relevant temperatures and salt concentrations. Our simulations for the first time confirm that XNA, having a near-orthogonal neucleobase pairing arrangement and a severely strained phosphate backbone, undergoes faster unzipping on the surface of a flat graphene sheet as compared to a ribonucleic acid (RNA) duplex with an identical sequence of the constituent nucleobases. The surface curvature and the topography of the carbon based nanomaterials are also crucial factors in determining the extent of binding interaction with double-stranded nucleotides, and our study indicates that XNA chain unwinding is comparatively faster on a flatter graphene surface as compared to on a convex single-walled carbon nanotube (SWCNT) of similar dimensions. This may be helpful in designing an efficient platform for delivering XNA into an infected human cell to function as an antisense or antigene probe. The effectiveness of such a technique is manifested in delivering a thermally and enzymatically more durable artificial nucleic acid that can be cleaved optimally into two oligonucleotides by a suitably modified graphene carrier in human serum for inhibiting specific gene expressions