Gold Nanoparticles as Efficient Scaffolds for Aptamer Adsorption: An In-silico Study

Aptasensors apply aptamers as recognition segments. Optical aptasensors are popular assays, due to highsensitivity. Gold nanoparticles (AuNPs) are efficient in developing aptasensors, due to easy synthesis andchemical stability. AuNPs are applied as fluorescence quencher or colorimetric indicator. Here, wetheoretically study the adsorption behavior of the tobramycin-specific aptamer on the AuNP surface bymolecular dynamics (MD) simulation to provide a confirmation on the ability of AuNP as an anchoragescaffold for aptamers, suitable for designing AuNPs-based aptasensors. The aptamer structure was obtainedfrom PDB (ID: ۱LC۴). To have its optimum conformation, ۶۰ ns MD simulation was done using GROMACS۲۰۱۸.۴. The simulated output was added to a simulation box containing a spherical AuNP with a radius of۲.۵ nm. ۱۱۰ ns MD simulation was performed considering AMBER-۹۹SB-IDLN force field for AuNP. TheRMSD graph reached a constant state about ۱۰۰ ns MD simulation, proved that ۱۱۰ ns was suitable for thestudy. The gyration radius (Rg) was approximately constant about ۲.۳ nm, very close to the AuNP radius,can be a sign for opening of the aptamer structure due to the adsorption on the AuNP surface. The RMSFproved the higher flexibility of the terminal nucleotides of the aptamer instead of the internal ones, inaccordance with the distances between the center of mass (COM) of each aptamer nucleotide and COM ofAuNP. Mean squared displacement (MSD) reflected the adsorption behavior of the aptamer, a potentanchoring of the aptamer on the AuNP surface after the simulation. The free energy landscape (FEL) analysisproved that the aptamer-AuNP complex is energetically favorable. Finally, the output observation by PyMOLsoftware illustrated the aptamer adsorption on AuNP with the effective role of the non-terminal nucleotides.

کلیدواژه ها:

Aptamer ، Gold nanoparticle ، Molecular dynamics simulation ، Free energy landscape