In this article, immobilized RNA aptamer on the gold nano particle surface was theoretically designed for selective detection of the neomycin B, neomycin C and paromomycin. Several molecular dynamic (MD) simulations on the pure aptamer, aptamer with –S(CH2)6- linker and immobilized aptamer on the gold nanoparticles surface were performed in the presence Neomycin B (NB). The obtained results indicate that the linker does not perturb the structure of the RNA aptamer. Also, full atomistic MD simulations on the immobilized RNA aptamer, as a biosensor, reveals a good sensing ability to ward neomycin B. On the basis of the DFT-D3 calculations, neomycin B forms a most stable complex with the aptamer binding site, due to the strong hydrogen bond formation. Moreover, the obtained results indicate that electrostatic interactions are the driving forces of complex formation.

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