Issue 45, 2009
From the journal:

Physical Chemistry Chemical Physics

Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by Brownian dynamics

Tomasz Wocjan,a   Jan Krieger,a   Oleg Krichevskyb  and  Jörg Langowski*a  

* Corresponding authors

a Biophysics of Macromolecules, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, Germany
E-mail: jl@dkfz-heidelberg.de

b Physics Department, Ben-Gurion University, Beer-Sheva, Israel

Abstract

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.

Graphical abstract: Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by Brownian dynamics

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Article information

DOI
https://doi.org/10.1039/B911857H
Article type
Paper
Submitted
16 Jun 2009
Accepted
21 Aug 2009
First published
16 Sep 2009

Phys. Chem. Chem. Phys., 2009,11, 10671-10681

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Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by Brownian dynamics

T. Wocjan, J. Krieger, O. Krichevsky and J. Langowski, Phys. Chem. Chem. Phys., 2009, 11, 10671 DOI: 10.1039/B911857H

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