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

Tomasz Wocjan, Jan Krieger, Oleg Krichevsky, Jörg Langowski

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

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.

Original languageEnglish
Pages (from-to)10671-10681
Number of pages11
JournalPhysical Chemistry Chemical Physics
Volume11
Issue number45
DOIs
StatePublished - 30 Nov 2009

ASJC Scopus subject areas

  • Physics and Astronomy (all)
  • Physical and Theoretical Chemistry

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