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

Abstract

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 nearorthogonal 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 carbonbased 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.

Understanding the Self-Assembling Behavior of Biological Building Block Molecules: A Spectroscopic and Microscopic Approach

“…The ability of such cross-seeding demands a better understanding of single amino acid self-assembly. Therefore, research related to the effect of chirality on morphologies 38,122 and the interactions between such assemblies with known nanomaterials like carbon nanotubes and graphene 123,124 would have been a key to enhancing this emerging field.…”

“…This type of membrane modulation by single metabolite assemblies can extend the approaches for understanding the self-reproduction phenomenon , which will further progress research into the origin of life. ,− Anand et al recently have shown that preformed single amino acid fibrils can enhance the aggregation of large proteins to develop toxic fibrils. , The ability of such cross-seeding demands a better understanding of single amino acid self-assembly. Therefore, research related to the effect of chirality on morphologies , and the interactions between such assemblies with known nanomaterials like carbon nanotubes and graphene , would have been a key to enhancing this emerging field.…”

Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers

“…This competition between ensembles makes XyNAs a potential molecular switch, and it is also a property unique to XyNAs among the known XNAs . Other recent MD studies of XyNA duplexes in the presence of a carbon nanotube have demonstrated fast spontaneous unzipping as a consequence of the strained backbone, highlighting the potential of XyNAs in gene delivery for therapeutic purposes. , …”

“…13 Other recent MD studies of XyNA duplexes in the presence of a carbon 4 nanotube have demonstrated fast spontaneous unzipping as a consequence of the strained backbone, highlighting the promise of XyNAs with respect to gene delivery for therapeutic purposes. 22,23 In the present study, we use the computational potential energy landscape framework 24 to investigate the structural and dynamical properties of XyNA and dXyNA duplexes. The extensive sampling facilitated by discrete path sampling 25 (DPS) allows for the calculation of free energies and therefore proper comparison of the relative thermodynamic stabilities of the three major conformations expected, namely left-handed helical, right-handed helical and ladder-type structures.…”

A molecular device: A DNA molecular lock driven by the nicking enzymes

“…The use of nanomaterials to unzipping DNA/RNA has attracted widespread attention [44] , [45] and has important applications in gene therapy [46] , [47] , [48] , DNA computing [49] , [50] and other fields. Among them, the cutting characteristics of nicking enzymes [51] , [52] provide us with ideas for designing self-destructive molecular locks.…”