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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