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

Tomasz Wocjan; Jan Krieger; Oleg Krichevsky; Jörg Langowski

doi:10.1039/b911857h

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

Tomasz Wocjan, Jan Krieger, Oleg Krichevsky, Jörg Langowski

Department of Physics

Research output: Contribution to journal › Article › peer-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 language	English
Pages (from-to)	10671-10681
Number of pages	11
Journal	Physical Chemistry Chemical Physics
Volume	11
Issue number	45
DOIs	https://doi.org/10.1039/b911857h
State	Published - 30 Nov 2009

ASJC Scopus subject areas

General Physics and Astronomy
Physical and Theoretical Chemistry

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title = "Dynamics of a fluorophore attached to superhelical DNA: FCS experiments simulated by Brownian dynamics",

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.",

author = "Tomasz Wocjan and Jan Krieger and Oleg Krichevsky and J{\"o}rg Langowski",

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T2 - FCS experiments simulated by Brownian dynamics

AU - Wocjan, Tomasz

AU - Krieger, Jan

AU - Krichevsky, Oleg

AU - Langowski, Jörg

PY - 2009/11/30

Y1 - 2009/11/30

N2 - 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.

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

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