Regensburg 2010 – scientific programme

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BP: Fachverband Biologische Physik

BP 6: Posters: DNA and DNA Enzymes

BP 6.1: Poster

Monday, March 22, 2010, 17:15–20:00, Poster B1

Electrostatic effects in DNA cyclization and DNA looping by proteins — •Andrey Cherstvy — IFF-2, FZ Jülich, Germany

We calculate analytically the electrostatic energy of ring formation for highly charged DNA-like polyelectrolyte chain in the ground state [1]. We study how the degree of counterion condensation differs on small DNA rings as compared to Manning prediction for straight polyelectrolytes. We apply the model to analyze how cyclization factors of short DNAs are modified, as compared to Shimada-Yamakawa theory for neutral polymers. We also perform simple computer simulations to assess the free energy of end joining of fluctuating DNA at different salinities. We study also the looping of thin charged elastic filaments under applied torque and forces, using the elasticity theory equations [2]. We predict that larger twist rates are needed to create loops in charged cables as compared to neutral ones. We determine optimal shapes of charged loops at different salinities showing that at low salts more open loops are favored due to enhanced mutual repulsion of charges. This loop opening is consistent with results of recent computer simulations on formation of DNA loops by lac repressor.

[1] A. G. Cherstvy and R. Everaers, in preparation. [2] A. G. Cherstvy, submitted to JPCB.