Dresden 2006 – scientific programme

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AKB: Biologische Physik

AKB 40: Poster Session II

AKB 40.38: Poster

Wednesday, March 29, 2006, 16:30–19:30, P3

DNA elasticity and specific binding — •Nils Becker and Ralf Everaers — MPI Physik Komplexer Systeme, Dresden

In essential biological processes, DNA interacts with proteins in an indirect way. In some complexes the double helical structure of DNA remains intact, but is strongly deformed. Binding then depends on the deformability of the DNA. This indirect readout mechanism allows for binding to specific sequences based on their elasticity and structure.

An understanding of this kind of specific interaction requires detailed information about sequence-dependent DNA elasticity. Modeling DNA as a chain of rigid elements, the base pairs, this information can be encoded in elastic potentials between each step of two base pairs. Harmonic base pair step potentials have been determined in rather dissimilar ways from high-resolution structural data [1] and by molecular dynamics computer simulation of oligonucleotides [2].

We examine the relation of these two parametrizations. On this basis we give a measure for estimating how much the elastic deformation of a given base pair contributes to sequence specificity in a given complex. As a test case, we show results for the bacteriophage 434 repressor, a well-studied such complex [3], in which some base pairs are not contacted by the protein but still when mutated, greatly modify binding affinity.

[1] W. Olson et al., PNAS 95(19), 11163, 1998

[2] F. Lankas et al., Biophys J 85(5), 2872, 2003

[3] G.B. Koudelka et al., PNAS 85(13), 4633, 1988