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Issue 44, 2012
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Crowding effect on DNA melting: a molecular thermodynamic model with explicit solvent

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Abstract

A molecular thermodynamic model is developed to examine crowding effect on DNA melting. Each pair of nucleotides in double-stranded DNA and each nucleotide in single-stranded DNA are represented by two types of charged Lennard-Jones segments, respectively. Water molecules are mimicked explicitly as spherical particles, embedded in a dielectric continuum. Crowders with varying concentration, size, interaction strength, and chain length are considered. For DNA with a sequence of A20, the melting temperature is predicted to increase by 1 K in the presence of Ficoll70 and by 7.5 K in the presence of Ficoll70–polyvinyl pyrrolidone360 mixture. The predictions agree well with experimental data. Furthermore, the melting temperature is found to increase with increasing crowder size, but reduce with increasing interaction strength and crowder length. The predicted changes of Gibbs energy, entropy and enthalpy are consistent with experimentally measured values. The study reveals that DNA melting in a crowded environment is influenced by both entropic and enthalpic effects.

Graphical abstract: Crowding effect on DNA melting: a molecular thermodynamic model with explicit solvent

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Article information


Submitted
26 Jun 2012
Accepted
20 Sep 2012
First published
24 Sep 2012

Phys. Chem. Chem. Phys., 2012,14, 15400-15405
Article type
Paper

Crowding effect on DNA melting: a molecular thermodynamic model with explicit solvent

Y. Liu, Y. Shang, H. Liu, Y. Hu and J. Jiang, Phys. Chem. Chem. Phys., 2012, 14, 15400
DOI: 10.1039/C2CP42138K

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