Effect of Different Methanol Concentrations on dsDNA Structure： An Molecular Dynamics Simulation Study

The various thermodynamic macroscopic observables Root-mean-square fluctuation (RMSF) and root mean square deviation (RMSD) of nucleic acid backbone of 10 base-sequences of double-stranded DNA (dsDNA) of the P53 gene between 130 and 144 codon were studied using molecular dynamics (MD) simulations. The AMBER program was utilized to prepare the dsDNA structure of the p53 sequence and were studied using molecular dynamics (MD) simulations. MD simulations were carried out using Gromacs program. In this study, we Obtained the outcome of the properties of dsDNA system by different ensembles. The conical ensemble (NVT) and isobaric—isothermal (NPT) ensemble were employed to characterize the effect of different Methanol concentrations on dsDNA structure.