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Molecular Dynamics Investigation of the Interactions Between RNA Aptamer and Graphene-Monoxide/Boron-Nitride Surfaces: Applications to Novel Drug Delivery Systems

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Abstract

The interactions between RNA aptamer and boron nitride/graphene monoxide nanosheets were investigated using the molecular dynamics simulations. The potential capability of graphene monoxide and boron nitride surfaces to immobilize RNA aptamer was examined in detail. The distance between center of mass of RNA aptamer and the considered surfaces and root mean square deviation and fluctuation were calculated. The results suggest that the adsorption of RNA aptamer on the boron nitride surface is easily occurred compared to the adsorption on the graphene monoxide surface. Besides, RNA aptamer adsorption on the graphene monoxide nanosheet is energetically more favorable than that on the boron nitride one. The water molecules dipole moment and density profile were used to analyze water effect on the immobilization of aptamer on the GMO and BN surfaces. The results of all-atom molecular dynamics simulations show the higher ability of BN nanosheet for delivery application of this RNA aptamer.

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Acknowledgements

This work has been supported by Azarbaijan Shahid Madani University. [Grant number 214/D/25972]. The authors thank to Dr. Amirali Abbasi for valuable discussions and suggestions.

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Authors and Affiliations

  1. Molecular Simulation laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki, Jaber Jahanbin Sardroodi & Alireza Rastkar Ebrahimzadeh

  2. Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki, Jaber Jahanbin Sardroodi & Alireza Rastkar Ebrahimzadeh

  3. Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki & Jaber Jahanbin Sardroodi

  4. Department of Physics, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran

    Alireza Rastkar Ebrahimzadeh

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  1. Mohaddeseh Habibzadeh Mashatooki
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Habibzadeh Mashatooki, M., Sardroodi, J.J. & Ebrahimzadeh, A.R. Molecular Dynamics Investigation of the Interactions Between RNA Aptamer and Graphene-Monoxide/Boron-Nitride Surfaces: Applications to Novel Drug Delivery Systems. J Inorg Organomet Polym 29, 1252–1264 (2019). https://doi.org/10.1007/s10904-019-01089-0

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