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

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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 \(\sim 0.1~\hbox {M}\)) 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)\(_{15}\): (rU)\(_{15}\) or (rA)\(_{30}\): (rU)\(_{30}\) on graphene starts with the interaction between \(\pi \)-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)\(_{30}\): (rU)\(_{30}\) which keeps parallel arrangement along the graphene surface, the shorter one ((rA)\(_{15}\): (rU)\(_{15}\)) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)\(_{30}\): (rU)\(_{30}\) forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)\(_{15}\): (rU)\(_{15}\) 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.

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Data availability statement

This manuscript has no associated data or the data will not be deposited. [Authors’ comment: The data used to support the findings of this study are available from the corresponding author upon request.]

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Acknowledgements

This work has been supported by funding from the National Academy of Sciences of Ukraine under Grant 0120U100157. The authors acknowledge the Computational Center at B. I. Verkin Institute for Low Temperature Physics and Engineering for providing computer time.

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Authors and Affiliations

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

    Maksym V. Karachevtsev, Vladimir A. Valeev & Victor A. Karachevtsev

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  1. Maksym V. Karachevtsev
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  2. Vladimir A. Valeev
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Contributions

VAK conceived and designed the project. MVK took part in the project designing, performed the MD simulations and data analysis. VAV carried out the experiments. VAK and MVK prepared the figures and drafted the manuscript. All authors together approved the final manuscript.

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Correspondence to Maksym V. Karachevtsev.

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Karachevtsev, M.V., Valeev, V.A. & Karachevtsev, V.A. Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide. Eur. Phys. J. E 44, 24 (2021). https://doi.org/10.1140/epje/s10189-021-00030-z

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  • DOI: https://doi.org/10.1140/epje/s10189-021-00030-z

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