In this article, immobilized RNA aptamer on the gold nanoparticle surface was theoretically designed for selective detection of the neomycin B, neomycin C and paromomycin. Several molecular dynamic simulations on the pure aptamer, aptamer with –S(CH2 ) 6 – linker and immobilized aptamer on the gold nanoparticles surface were performed in the presence of diferent analytes. 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, reveal a good sensing ability toward neomycin B in the presence of paromomycin and neomycin C. Due to complex formation, the distance of the aptamer and gold nanoparticles decreases. Moreover, the analysis of the electrostatic interactions between the aptamer and neomycin B shows a reduction in the tendency of the aptamer to interact with the gold nanoparticles, signifcantly. On the basis of the DFT-D3 calculations, neomycin B forms the 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. On the basis of QM/MD results, the proposed aptasensor is a good candidate for the detection of neomycin B.

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