Different sensors composed of aptasensor have been largely designed for detection of many analytes recently due to the ease of detection, high sensitivity, and potential for high-throughput analysis. In this article, a joint theoretical and experimental study was performed to design new gold nanoparticle based colorimetric aptasensor. At the first step, by employing molecular dynamic (MD) simulations, twenty new RNA aptamers for detection of neomycin B (NB) were theoretically designed. The sensing ability and their binding affinity of these aptamers toward NB were investigated from the theoretical viewpoint and the predicted behaviors were compared with that of the wild type aptamer (AP-W). Theoretical results indicated that two aptamers of AP-M18 and AP-M20 have a greater affinity toward NB in comparison with AP-W. At the next step, AP-M18, AP-M20 and AP-W were synthesized and their affinity and selectivity toward NB were investigated by gold nanoparticles (AuNPs) based colorimetric method. On the basis of experimental results, the calculated limit of detection (LOD) values of AP-M18 and AP-M20 are 27 and 360 nM, respectively, which are lower than that of AP-W (470 nM). Moreover, quantum chemistry calculations indicated that van der Waals and electrostatic interactions may be the driving force of the NB complexation. A greater affinity of AP-M18 against NB can be explained by the possible stronger donor-acceptor interactions. A good agreement between different predicted properties with the experimental results suggests the ability of the theoretical methods to design new aptamers for detection of various targets.

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