1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Gold Nanoparticles as Efficient Scaffolds for Aptamer Adsorption: An In-silico Study
Paper ID : 1452-ICB10
Authors:
Hamed Zahraee1, Zahra Khoshbin *2, Mohammad Reza Bozorgmehr3
1گزوه زیست شناسی، دانشکده علوم، دانشگاه فردوسی مشهد، ایران
2گروه شیمی دارویی، دانشکده داروسازی، دانشگاه علوم پزشکی مشهد، ایران
3گروه شیمی، دانشکده علوم پایه، دانشگاه آزاد اسلامی، مشهد، ایران
Abstract:
Aptasensors apply aptamers as recognition segments. Optical aptasensors are popular assays, due to high sensitivity [1]. Gold nanoparticles (AuNPs) are efficient in developing aptasensors, due to easy synthesis and chemical stability. AuNPs are applied as fluorescence quencher or colorimetric indicator [2]. Here, we theoretically study the adsorption behavior of the tobramycin-specific aptamer on the AuNP surface by molecular dynamics (MD) simulation to provide a confirmation on the ability of AuNP as an anchorage scaffold for aptamers, suitable for designing AuNPs-based aptasensors. The aptamer structure was obtained from PDB (ID: 1LC4). To have its optimum conformation, 60 ns MD simulation was done using GROMACS 2018.4. [3,4] The simulated output was added to a simulation box containing a spherical AuNP with a radius of 2.5 nm. 110 ns MD simulation was performed considering AMBER-99SB-IDLN force field for AuNP [5]. The RMSD graph reached a constant state about 100 ns MD simulation, proved that 110 ns was suitable for the study. The gyration radius (Rg) was approximately constant about 2.3 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 RMSF proved the higher flexibility of the terminal nucleotides of the aptamer instead of the internal ones, in accordance with the distances between the center of mass (COM) of each aptamer nucleotide and COM of AuNP. Mean squared displacement (MSD) reflected the adsorption behavior of the aptamer, a potent anchoring of the aptamer on the AuNP surface after the simulation. The free energy landscape (FEL) analysis proved that the aptamer-AuNP complex is energetically favorable. Finally, the output observation by PyMOL software [6] illustrated the aptamer adsorption on AuNP with the effective role of the non-terminal nucleotides.
Keywords:
Aptamer; Gold nanoparticle; Molecular dynamics simulation; Free energy landscape.
Status : Paper Accepted (Poster Presentation)