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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 16: POSTERS Polyelectrolytes and Biological Systems

CPP 16.18: Poster

Dienstag, 24. März 2009, 14:00–16:30, P3

Calculation of the helical interaction parameters and groove binding potentials for DNA like charged cylinders. — •Dominic Lee — Max-Planck Institut für Physik Komplexer Systeme, Nöthnizer Str. 38, D-01187, Dresden, Germany

An effective (KL) theory was developed to calculate the interaction between helically charged macro-ions [1]. Helical effects, resulting from this theory, may be important in cholesteric phases and in columnar assemblies [1]. It relies upon a "linearized" PB equation; but non-linearities in the electrostatic potential, bound counter-ions, finite sizes of ions, and some correlation effects can be included in effective KL parameters. These define the strength of the helical contributions to the interaction, which have so far been treated as phenomenological. However, the KL parameters can be calculated if one knows the counter-ion charge and fixed charge distributions about a single macro-ion [1]. We briefly review the KL theory. Then, we calculate these parameters utilizing a model of a charged cylinder with DNA like surface distributions, taking into account counter-ions adsorbed within the grooves of DNA. We use two methods: the non-linear PB equation and a modified PB equation that incorporates some correlation and finite size effects that adjust the counter ion atmosphere. The distributions of groove-adsorbed counter-ions are related to groove binding potentials, by calculation of an adsorption isotherm.

[1]A.A Kornyshev, D. J. Lee, S. Leikin, A. Wynveen, Rev. Mod. Phys. 79, 943 (2007); and references contained therein.; EPAPS Doccument No. E-RMPHAT-79-010702