Unwinding DNA strands by Single-Walled Carbon Nanotubes: Molecular docking and MD simulation approach - Université Clermont Auvergne
Article Dans Une Revue Journal of Molecular Graphics and Modelling Année : 2024

Unwinding DNA strands by Single-Walled Carbon Nanotubes: Molecular docking and MD simulation approach

Résumé

Despite the growing research into the use of carbon nano-tubes (CNTs) in science and medicine, concerns about their potential toxicity remain insufficiently studied. This study utilizes molecular docking calculations combined by molecular dynamics simulations to investigate the dynamic intricacies of the interaction between single-walled carbon nanotubes (swCNTs) and doublestranded DNA (dsDNA). By examining the influence of swCNT characteristics such as length, radius, and chirality, our findings shed light on the complex interplay that shapes the binding affinity and stability of the dsDNA-swCNT complex. Molecular docking results identify a zigzag swCNT, with a radius of 0.16 Å and a length of 38 Å, as exhibiting the highest binding affinity with dsDNA (-23.9 kcal/mol). Comprehensive analyses, spanning docking results, binding energies, RMSD, radius of gyration, and potential of mean force (PMF) profiles, provide a detailed understanding of the denaturation dynamics. The PMF profiles reveal the thermodynamic feasibility of the DNA-CNT interaction, outlining distinct energy landscapes and barriers: when the selected swCNT binds within the dsDNA groove, the system becomes trapped at the first and second local energy minima, occurring at 1.48 nm and 1.00 nm, respectively. Intramolecular hydrogen bond calculations show a significant reduction, affirming the denaturing effect of swCNTs on DNA. Furthermore, the study reveals a significant reduction in the binding affinity of Ethidium Bromide (EB) to dsDNA following its interaction with swCNT, with a decrease in EB binding to dsDNA of approximately 13.2%. This research offers valuable insights into the toxic effects of swCNTs on dsDNA, contributing to a rationalization of the cancerous potential of swCNTs.
Fichier principal
Vignette du fichier
Sahihi_Manuscript_JMGM_R1_clear.pdf (809.65 Ko) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)

Dates et versions

hal-04735180 , version 1 (14-10-2024)

Identifiants

Citer

Ghazal Borhan, Mehdi Sahihi. Unwinding DNA strands by Single-Walled Carbon Nanotubes: Molecular docking and MD simulation approach. Journal of Molecular Graphics and Modelling, In press, 133, pp.108882. ⟨10.1016/j.jmgm.2024.108882⟩. ⟨hal-04735180⟩
19 Consultations
17 Téléchargements

Altmetric

Partager

More