Exploring the Interaction of Oligonucleotides with Single-Walled Carbon Nanotube as industrial bio-catalysis: A Molecular Dynamics Simulation Study
Mohammad Reza Bozorgmehr
1
(
Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
)
Maryam Ghanbari-Ghanbarlo
2
(
Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
)
Ali Morsali
3
(
Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
)
Keywords: detection, polymer, Biosensor, Nanotube, organic base,
Abstract :
In this research, the interaction of four single stranded nucleic acid homopolymers including hemo deca adenine, dA10, hemo deca thymine, dT10, hemo deca guanine, dG10 and hemo deca cytosine, dC10, with single-walled carbon nanotubes was studied by molecular dynamics simulation method. The simulations were performed using Gromacs software and Amber force field, with a simulation time of 250 nanoseconds and 2 femtosecond time step. The root mean square deviation (RMSD) values were calculated to validate the simulations, indicating that the systems reached equilibrium. The distance between the center of mass of the homo deca polymers and the surface of the carbon nanotube was also calculated, and the results showed that the interaction of monocyclic organic bases with the nanotubes was higher due to less steric hindrance with the phosphate group. The results suggest that monocyclic organic bases may be more suitable for interactions with carbon nanotubes due to their lower steric hindrance.