12th Carl Zeiss sponsored workshop on ... - Institut Fresnel

Dynamics of supercoiled DNA studied by FCS and computer modeling
Tomasz Wocjan 1 , Jan Krieger 1 , Oleg Krichevsky 2 and Jörg Langowski 1
1
Biophysics of Macromolecules, German Cancer Research Center, Im Neuenheimer Feld
580, 69120 Heidelberg, Germany
2
Physics Department, Ben-Gurion University, Beer-Sheva 84105, Israel
The organization of the genome in the cell nucleus is fundamental for cellular function:
transcription and its regulation, genome duplication, epigenetic effects and chromosome
folding are all intricately connected to genome architecture. On the lowest level of genome
organization, DNA folding is determined by its bending and twisting properties; superhelical
DNA is a well-known model system to study these properties. Recent experiments by
fluorescence correlation spectroscopy (Shusterman et al., (1008) Phys Rev Lett. 100:098102)
indicated a sensitivity of the monomer mean square displacements in DNA circles towards
superhelicity. To explain this phenomenon, we investigated the dynamics of a singlefluorophore-labeled
pUC18 plasmid through a Brownian dynamics algorithm, followed by a
simulation of the fluorescence correlation spectroscopy (FCS) process. Simulations with
homogeneous DNA elasticity and local straight equilibrium are not sufficient to reproduce the
observed behavior. But inserting permanently bent sequences into the DNA, which favor end
loop formation, caused a dependence of the calculated FCS correlation curves on superhelical
density. Furthermore, our simulations allow us to take into account the orientation of the
fluorophore in polarized excitation, which might explain the observed appearance of a Rouselike
regime at intermediate time scales.