Spontaneous Unzipping of Xylonucleic Acid Assisted by a Single-Walled Carbon Nanotube: A Computational Study.

Abstract

Xenonucleic acids are synthetic nucleic acid analogues that are potential candidates for antisense or antigene therapy owing to their higher thermal and enzymatic stability compared to that of naturally occurring ones at physiological conditions. We investigate the binding and unzipping of xylonucleic acid (XNA) containing xylose (a stereoisomer of ribose) sugar in its backbone assisted by a single walled carbon nanotube (SWCNT) using extensive atomistic molecular dynamics simulations. Our simulations confirm XNA to undergo faster unzipping compared to a double stranded RNA with the same nucleobase sequence which is presumably due to the near orthogonal base pairing arrangement of the constituent nucleobases of XNA at physiologically relevant conditions (in terms of temperature and salt concentration). The interaction between XNA and SWCNT mimics that of a small interfering RNA (siRNA) and RNA-induced silencing complex (RISC) during a typical RNA induced gene silencing process where the duplex chain unwinding of the siRNA is of primordial importance. Our study may find relevance in designing a more efficient and safer delivery platform for xenonucleic acids by grafting these RNA analogues to SWCNT into an infected target cell. This unveils promising applications of XNA in the field of gene delivery for antisense therapies.