Eur. Phys. J. E (2021) 44: 24
https://doi.org/10.1140/epje/s10189-021-00030-z

Regular Article - Soft Matter

Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide

B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., 61103, Kharkiv, Ukraine

^a mkarachevtsev@ilt.kharkov.ua

Received: 16 November 2020
Accepted: 29 January 2021
Published online: 8 March 2021

Abstract

Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of ) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA): (rU) or (rA): (rU) on graphene starts with the interaction between -systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA): (rU) which keeps parallel arrangement along the graphene surface, the shorter one ((rA): (rU)) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA): (rU) forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA): (rU) demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.