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DNA-DNA interactions in tight supercoils are described by a small effective charge density.


ABSTRACT: DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.

SUBMITTER: Maffeo C 

PROVIDER: S-EPMC3170404 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

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DNA-DNA interactions in tight supercoils are described by a small effective charge density.

Maffeo Christopher C   Schöpflin Robert R   Brutzer Hergen H   Stehr René R   Aksimentiev Aleksei A   Wedemann Gero G   Seidel Ralf R  

Physical review letters 20101004 15


DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is  ...[more]

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