Jump to main content
Jump to site search

Issue 45, 2009
Previous Article Next Article

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

Author affiliations

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

Back to tab navigation

Publication details

The article was received on 16 Jun 2009, accepted on 21 Aug 2009 and first published on 16 Sep 2009


Article type: Paper
DOI: 10.1039/B911857H
Citation: Phys. Chem. Chem. Phys., 2009,11, 10671-10681
  •   Request permissions

    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

Search articles by author

Spotlight

Advertisements