Non-Covalent Hybridization of Carbon Nanotube by Single-Stranded DNA Homodecamers: in-silico Approach

• Published in: Russian Journal of Physical Chemistry A 2022, Vol.96 (1), p.145-151
• Main Authors: Ghanbari-Ghanbarlo, Maryam, Bozorgmehr, Mohammad Reza, Morsali, Ali
• Format: Article
• Language: English
• Subjects: Carbon; Chains; Chemistry; Chemistry and Materials Science; Free energy; Molecular conformation; Molecular dynamics; Oligonucleotides; Physical Chemistry; Physical Chemistry of Nanoclusters and Nanomaterials; Single wall carbon nanotubes
• ISSN: 0036-0244; 1531-863X
• DOI: 10.1134/S0036024422010125

The interaction of oligonucleotides dA10, dC10, dG10, and dT10 with single-walled carbon nanotube was investigated using molecular dynamics simulation. The distance of the mass center of each of the oligonucleotides with the carbon nanotube axis was calculated. The results show that this distance is as dA10 > dG10 > dC10 > dT10. The conformation of the main chain and single-stranded DNA side chain were investigated using pseudo angles (η, θ) and (χ, P ) respectively. The results show that the interaction of the CNT with the main chain of oligonucleotides occurs from the region , which is related to the angle η. The rotation of purine bases has also occurred more than the pyrimidine bases. The free energy analysis of interaction compared to the two distance criteria of end-to-end oligonucleotides and the number of residues that have π–π interaction with nanotubes shows that each of the four decamers has a π–π interaction with nanotubes. Nevertheless, their π–π interaction regions are at the end of the decamer for purine bases and in the first and middle regions for the pyrimidine bases. The results are in good agreement with the experimental data and the results of other simulations.