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Keywords
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Drug Delivery, RNA Aptamer, BNNT, Biocompatible, Molecular Dynamics
Simulation.
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Abstract
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RNA aptamers have been attractively attentioned in the recent years by researchers. In comparison
to the antibodies they have numerous advantages such as high specificity and affinity that made them an
excellent agent in order to identify and decrease diseased cells in the blood stream [1] . Molecular information
such as energetics of the interaction and structure of the drug-nanoparticle complex have critical importance
in design smart delivery systems for cancer therapy [2] . Here, we have investigated the molecular interaction
of RNA aptamer with (12,12) boron-nitride nanotube (BNNTs), excellent biocompatible and non-toxic
nanotube [3] . We prepared complexes composed from a RNA aptamer that has been selected and
tested experimentally by Na Li et all [4] as an binding agent to Epidermal Growth Factor Receptor
(EGFR) and (12,12) BNNT. Then we simulated them by NAMD package [5] with CHARMM-36 force field
along 60 simulation time with 1 fs time steps. The results of the simulation were analyzed as structural
parameters like differences of the centers of mass, the radial distribution functions, the radius of gyration,
the root mean square deviation and so on. Along with the structural analysis, we carried on the energetics
analysis including the non-boning interaction energies and the contributions of electrostatic and van der
Waals interactions between aptamer and BNNT. The results show that the adsorption of aptamer on BNNT
has not destructive effect on the aptamer structure and its configuration restore in adsorbed state. On the
other hand, the release of aptamer from BNNT is not probably a difficult process, because the interaction
energies (adsorption energies, in other terms) are not so large. Therefor the studied BNNT can be used as a
delivery system for considered RNA aptamer at the studied conditions.
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