Molecular Insight into the Adsorption of Tobramycin Specific Aptamer on Graphene Sheet

Aptasensors are biosensors based on aptamers as the bio-recognition. Graphene is a two-dimensional carbonsheet, attractive for the design of fluorescence and electrochemical aptasensors. Graphene provides someanchorage sites for aptamers; hence, we theoretically study the adsorption behavior of the tobramycinspecificaptamer on graphene by molecular dynamics (MD) simulation to provide a molecular confirmationon the aptamer adsorption by graphene, suitable for the design of graphene-based aptasensors. To have aninitial aptamer (PDB ID: ۱LC۴) configuration, ۲۵ ns MD simulation was done using GROMACS ۲۰۱۸.۴[۵,۶] with CHARMM۳۶-jul۲۰۲۱ force field. The output was added to a simulation box containing a graphenesheet, and ۱۹۰ ns MD simulation was performed. The decrease in the RMSD fluctuations proved the steadyadsorption of the aptamer on the sheet. The RMSF analysis proved the higher flexibility of the nucleotidesat the ۳´-region in comparison with that at the ۵´-region. Indeed, the aptamer adsorption was first happenedthrough its ۵´-region, and then, its ۳´-end, in accordance with the distance between the center of mass (COM)of each nucleotide and graphene along the Z-axis. Mean squared displacement (MSD) parameter reflectedthe adsorption behavior of the aptamer, a potent anchoring of the aptamer on the graphene surface after thesimulation. The free energy landscape (FEL) proved that the aptamer-graphene complex was energeticallyfavorable. The reduced density gradient (RDG) analysis clarified that the hydrogen bonding and van derWaals interactions played an important role in the aptamer adsorption on graphene. Finally, the outputobservation by PyMOL software illustrated that the aptamer was first adsorbed through its ۵´-region, andthen, its ۳´-region, and finally, its structure was completely located on the graphene surface.

کلیدواژه ها:

Adsorption ، Aptamer ، Graphene ، Molecular dynamics simulation ، Tobramycin