Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 11, Issue 45, Pages 10671-10681Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/b911857h
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Funding
- German Science Foundation (DFG) [La 500/14]
- German-Israeli Foundation (GIF) [972-146.14/2007]
- International Graduate College [IGK 710]
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We investigated the dynamics of a single-fluorophore-labeled pUC18 plasmid through a Brownian dynamics algorithm, followed by a simulation of the fluorescence correlation spectroscopy (FCS) process. Recent experimental FCS measurements indicated a sensitivity of the monomer mean square displacements in DNA circles towards superhelicity. Simulations with homogeneous DNA elasticity and local straight equilibrium are not sufficient to reproduce this 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 Rouse-like regime at intermediate time scales.
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