Dresden 2006 – scientific programme

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AKB: Biologische Physik

AKB 26: Cellular Computation and Gene Regulation

AKB 26.2: Talk

Friday, March 31, 2006, 11:30–11:45, ZEU 255

Optimal target search on a fast folding DNA with volume exchange — •Ralf Metzler, Michael Lomholt, and Tobias Ambjoernsson — NORDITA, Blegdamsvej 17, DK-2100 Copenhagen

We study the search process of a target on a rapidly folding DNA by an ensemble of proteins, whose search combines 1D diffusion along the chain, Lévy type diffusion [1] mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search. Thus, it turns out that the Lévy search component leads to much more efficient target search and under certain conditions renders 3D volume diffusion obsolete [2]. The model includes the special cases of the ‘standard’ 3D/1D exchange [3] as well as pure 1D search [4]. The model is expected to pertain to typical in vivo studies of genetic regulation, and predicts significantly higher targeting rates than previous models. It is suggested that the Lévy contribution can be studied experimentally under low salt conditions disfavouring protein unbinding from the DNA.

[1] R. Metzler and J. Klafter, Phys. Rep. 339, 1 (2000); J. Phys. A 37 R161 (2004).

[2] M.A. Lomholt, T. Ambjörnsson, and R. Metzler, subm. to Phys. Rev. Lett.; E-print cond-mat/0510072.

[3] M. Coppey, O. Benichou, R. Voituriez, and M. Moreau, Biophys. J. 87, 1640 (2004).

[4] I. M. Sokolov, R. Metzler, K.Pant, and M. C. Williams, Biophys. J. 89, 895 (2005).