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 infect...

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