Dresden 2014 – scientific programme

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BP: Fachverband Biologische Physik

BP 13: Posters: DNA/RNA and related enzymes

BP 13.6: Poster

Tuesday, April 1, 2014, 09:30–12:30, P1

Effects of molecular crowding on promoter finding — •David Gomez and Stefan Klumpp — Max Planck Institute of Colloids and Interfaces, Potsdam, Germany

All biological functions of DNA depend on the recognition of specific sequences by site-specific DNA-binding proteins. Binding of these proteins to their binding sites is believed to occur through a facilitated diffusion process that combines one-dimensional diffusion along the DNA with three-dimensional diffusion in the bulk solution.

This model has been assumed to be general for all DNA-binding proteins even though the conditions, such as protein concentrations, are different for different DNA-binding proteins. The objective of this work is to model the dynamics of the RNAP-promoter binding under different concentrations of RNAPs and other proteins that act as `obstacles.' To do that, we place a linear DNA template with its promoter, RNAPs and obstacles on a 3D lattice, and determine the RNAP-promoter binding rates at different conditions. Our results suggest that an acceleration in the binding process occurs only at some obstacle concentrations and non-specific binding times of the RNAP on the DNA.