We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a “piston”—a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the “piston”: while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they “pop-off” one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
Skip Nav Destination
Article navigation
28 July 2017
Research Article|
July 31 2017
Entropic elasticity and dynamics of the bacterial chromosome: A simulation study
M. C. F. Pereira;
M. C. F. Pereira
1
SUPA, School of Physics and Astronomy, University of Edinburgh
, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
Search for other works by this author on:
C. A. Brackley;
C. A. Brackley
1
SUPA, School of Physics and Astronomy, University of Edinburgh
, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
Search for other works by this author on:
J. S. Lintuvuori;
J. S. Lintuvuori
2
Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Universite Paris-Saclay
, 91405 Orsay Cedex, France
Search for other works by this author on:
D. Marenduzzo;
D. Marenduzzo
1
SUPA, School of Physics and Astronomy, University of Edinburgh
, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
Search for other works by this author on:
E. Orlandini
E. Orlandini
3
Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova
, Via Marzolo 8, Padova, 35131 PD, Italy
Search for other works by this author on:
J. Chem. Phys. 147, 044908 (2017)
Article history
Received:
March 17 2017
Accepted:
July 13 2017
Citation
M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo, E. Orlandini; Entropic elasticity and dynamics of the bacterial chromosome: A simulation study. J. Chem. Phys. 28 July 2017; 147 (4): 044908. https://doi.org/10.1063/1.4995992
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
Dielectric profile at the Pt(111)/water interface
Jia-Xin Zhu, Jun Cheng, et al.
Related Content
Physics of the Bacterial Chromosome
AIP Conference Proceedings (January 2006)
Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins
J. Chem. Phys. (February 2018)
Bacterial chromosome organization. II. Few special cross-links, cell confinement, and molecular crowders play the pivotal roles
J. Chem. Phys. (April 2019)
Collapse transition of a heterogeneous polymer in a crowded medium
J. Chem. Phys. (August 2021)