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• W2045703103 abstract "We discuss the effectiveness of existing methods for understanding the forces driving the formation of specific protein-DNA complexes. Theoretical approaches using the Poisson-Boltzmann (PB) equation to analyse interactions between these highly charged macromolecules to form known structures are contrasted with an empirical approach that analyses the effects of salt on the stability of these complexes and assumes that release of counter-ions associated with the free DNA plays the dominant role in their formation. According to this counter-ion condensation (CC) concept, the salt-dependent part of the Gibbs energy of binding, which is defined as the electrostatic component, is fully entropic and its dependence on the salt concentration represents the number of ionic contacts present in the complex. It is shown that although this electrostatic component provides the majority of the Gibbs energy of complex formation and does not depend on the DNA sequence, the salt-independent part of the Gibbs energy--usually regarded as non-electrostatic--is sequence specific. The CC approach thus has considerable practical value for studying protein/DNA complexes, while practical applications of PB analysis have yet to demonstrate their merit." @default.
• W2045703103 created "2016-06-24" @default.
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• W2045703103 creator A5019868363 @default.
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• W2045703103 date "2010-11-10" @default.
• W2045703103 modified "2023-10-10" @default.
• W2045703103 title "Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components" @default.
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• W2045703103 doi "https://doi.org/10.1093/nar/gkq984" @default.
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