Keywords

Molecular dynamics, Electrostatics, Ions and properties, Chemical elements, Polymers, Phosphates, Fluid bubbles, Nucleotides, Coarse-grain model, Proteins

Abstract

Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.

Original Publication Citation

T. A. Knotts IV, N. Rathore, David C. Schwartz, and J. J. de Pablo, A Coarse Grain Model for DNA, J. Chem. Phys., 126, 084901 (2007) (Most Downloaded JCP Article, Feb 07).

Document Type

Peer-Reviewed Article

Publication Date

2007-02-23

Publisher

AIP Publishing

Language

English

College

Ira A. Fulton College of Engineering

Department

Chemical Engineering

University Standing at Time of Publication

Full Professor

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