Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

ABSTRACT: Essential biological processes require that proteins bind to a set of specific DNA sites with tuned relative affinities. We focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of DNA elasticity on the rigid base pair level. Combining existing parametrizations of elastic potentials for DNA, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker for elastically optimized subsequences in protein-DNA co-crystals. We test our approach in an application to the bacteriophage 434 repressor. In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site. Elastic optimization involves

SUBMITTER: Becker NB 

PROVIDER: S-EPMC1636474 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature