مشخصات پژوهش

The interactions of nanoparticles with single stranded nucleic acids (NAs) have important implications ranged from drug and gene delivery to nano-machine building to bio-sensor design and productions [1] . Therefore, in this research work, we investigate the interactions of a gold nanosheet as drug carrier with RNA aptamer as anti-HIV drug acting as inhibitor for HIV-1 protease by molecular dynamics simulation method. All molecular dynamics simulations were performed using the NAMD-2.12 software [2] and the visualizations and analyzing of MD trajectories were executed by VMD-1.9.2 package [3] . Three sequences families of RNA aptamers were selected. Recently, [4] studied these aptamers experimentally and reported anti-HIV properties for them. The Second-generation RNA aptamers were selected from Kinefolde web server. The third structures predicted by SIMRNA web server are in agreement with the experimental data. The interactions between GNP and considered aptamers have been studied by extracting the structural and energetics results from the simulation trajectories. The structural data are like RMSD, hydrogen bonds and center of mass distances were used for elucidation of the adsorption and immobilization of aptamer on the gold nanosheets as well as its native folded structue. Enetrgerics of the interactions such as total inteaction energy and the contribution of van der Waals and electrostatic interactions in total energy were used for estimation of the adsorption strength of studied aptamers in the binded fashion. These results could give insights into the flexibility of aptamer sequences the qualitative information about the conformational changes of the aptamer’s backbone along the simulation time. These values were in a reasonable range and indicated the native structure of aptamer remained along the simulation. The intraction residues were verifed by the help of the averaged RMSF values for intraction and nonintraction aptamers accompanying conventional visual