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Molecular Dynamics Simulation of a Single Stranded (ss) DNA

S. Chatterjee, B. Gersten, S. Thakur and A. Burin
Queens College, CUNY, US

Keywords:
molecular dynamics, single stranded DNA, p53 gene

Abstract:
The objective of this study was to develop an understanding of the essential physical properties of short-single stranded DNA (ssDNA) towards the development of new DNA based biosensors. To achieve this goal, various thermodynamic properties (pressure, specific heat, and temperature and energy distribution) and structural features (Root mean square deviation (RMSD) of nucleic acid, end to end distribution) of 15 codon sequences (between 130 and 144) of the P53 gene were studied using Molecular Dynamics (MD) Simulation. AMBER was utilized to prepare the ssDNA structure of the p53 sequence and MD simulations were carried out using NAMD program. The micro canonical ensemble (NVE) and conical ensemble (NVT) and Constant Pressure -Temperature (NPT) ensemble were employed to characterize the equilibrium behavior of ssDNA in aqueous solution. In this study, we compared the outcome of thermodynamic properties of ss DNA by three different ensembles. Our study illustrated the distinguishable structural and electronic features of the ssDNA that have a great impact on controlling the hybridization phenomenon, necessary for successful development of novel biosensors.

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