Molecular dynamics simulations of a single stranded (ss) DNA

S. Chatterjee; B. Gersten; S. Thakur; A. Burin

doi:10.1080/08927020601067524

Molecular dynamics simulations of a single stranded (ss) DNA

S. Chatterjee, B. Gersten, S. Thakur, A. Burin

Chemistry

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

The objective of this study was to develop an understanding of short-single stranded DNA (ssDNA) to aid the development of new DNA-based biosensors. The various thermodynamic macroscopic observables (temperature and energy distributions) and root mean square deviation (RMSD) of nucleic acid backbone of 12 base-sequences of ssDNA of the P53 gene between 130 and 144 codon were studied using molecular dynamics (MD) simulations. The AMBER program was utilized to prepare the ssDNA structure of the p53 sequence and MD simulations were carried out using NAMD program. In this study, we compared the outcome of the properties of ssDNA system by different ensembles. The microcanonical ensemble (NVE) and conical ensemble (NVT) and isobaric - isothermal (NPT) ensemble were employed to characterize the equilibrium behavior of ssDNA in aqueous solution.

Original language	English
Pages (from-to)	573-576
Number of pages	4
Journal	Molecular Simulation
Volume	33
Issue number	7
DOIs	https://doi.org/10.1080/08927020601067524
State	Published - Jun 2007

Keywords

Biosensor
Molecular dynamics
RMSD
ssDNA

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10.1080/08927020601067524

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AU - Gersten, B.

AU - Thakur, S.

AU - Burin, A.

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AB - The objective of this study was to develop an understanding of short-single stranded DNA (ssDNA) to aid the development of new DNA-based biosensors. The various thermodynamic macroscopic observables (temperature and energy distributions) and root mean square deviation (RMSD) of nucleic acid backbone of 12 base-sequences of ssDNA of the P53 gene between 130 and 144 codon were studied using molecular dynamics (MD) simulations. The AMBER program was utilized to prepare the ssDNA structure of the p53 sequence and MD simulations were carried out using NAMD program. In this study, we compared the outcome of the properties of ssDNA system by different ensembles. The microcanonical ensemble (NVE) and conical ensemble (NVT) and isobaric - isothermal (NPT) ensemble were employed to characterize the equilibrium behavior of ssDNA in aqueous solution.

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Molecular dynamics simulations of a single stranded (ss) DNA

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Keywords

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