Nonspecific DNA-protein interaction: why proteins can diffuse along DNA

Dahirel, Vincent and Paillusson, Fabien and Jardat, Marie and Barbi, Maria and Victor, Jean-Marc (2009) Nonspecific DNA-protein interaction: why proteins can diffuse along DNA. Physical Review Letters, 102 (22). ISSN 0031-9007

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Abstract

Recent single molecule experiments have reported that DNA binding proteins (DNA-BPs) can diffuse along DNA. This suggests that interactions between proteins and DNA play a role during the target search even far from their specific site on DNA. Here we show by means of Monte Carlo simulations and analytical calculations that there is a counterintuitive repulsion between the two oppositely charged macromolecules at a nanometer range. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the DNA-protein interaction free energy has a minimum at a finite surface-to-surface separation, in which proteins can easily slide. When a protein encounters its target, the free energy barrier is completely counterbalanced by the H-bond interaction, thus enabling the sequence recognition.

Keywords:DNA, Electrostatics, Proteins
Subjects:F Physical Sciences > F300 Physics
F Physical Sciences > F170 Physical Chemistry
Divisions:College of Science > School of Mathematics and Physics
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ID Code:17973
Deposited On:09 Sep 2015 05:15

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