Unwrapping of DNA-protein complexes under external stretching

Takahiro Sakaue, Hartmut Löwen

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

A DNA-protein complex modeled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without a stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and dynamics of the unwrapping process by computer simulations and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered; i.e., there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent of nucleosome. There is a clear winding number, and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated with discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.

Original languageEnglish
Number of pages1
JournalPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
Volume70
Issue number2
DOIs
Publication statusPublished - Jan 1 2004

Fingerprint

deoxyribonucleic acid
proteins
Protein
monomers
Optical Tweezers
Winding number
Curve
curves
Complex Structure
stiffness
Stiffness
Jump
Computer Simulation
computerized simulation
Linearly
Scenarios
Prediction
predictions
Experiment

All Science Journal Classification (ASJC) codes

  • Statistical and Nonlinear Physics
  • Mathematical Physics
  • Condensed Matter Physics
  • Physics and Astronomy(all)

Cite this

Unwrapping of DNA-protein complexes under external stretching. / Sakaue, Takahiro; Löwen, Hartmut.

In: Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, Vol. 70, No. 2, 01.01.2004.

Research output: Contribution to journalArticle

@article{8c46fe2af4b74dc5838f8e3ef71c507e,
title = "Unwrapping of DNA-protein complexes under external stretching",
abstract = "A DNA-protein complex modeled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without a stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and dynamics of the unwrapping process by computer simulations and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered; i.e., there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent of nucleosome. There is a clear winding number, and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated with discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.",
author = "Takahiro Sakaue and Hartmut L{\"o}wen",
year = "2004",
month = "1",
day = "1",
doi = "10.1103/PhysRevE.70.021801",
language = "English",
volume = "70",
journal = "Physical Review E",
issn = "2470-0045",
publisher = "American Physical Society",
number = "2",

}

TY - JOUR

T1 - Unwrapping of DNA-protein complexes under external stretching

AU - Sakaue, Takahiro

AU - Löwen, Hartmut

PY - 2004/1/1

Y1 - 2004/1/1

N2 - A DNA-protein complex modeled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without a stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and dynamics of the unwrapping process by computer simulations and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered; i.e., there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent of nucleosome. There is a clear winding number, and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated with discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.

AB - A DNA-protein complex modeled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in space. Without a stretching force, the chain is wrapped around the core. By applying an external stretching force, unwrapping of the complex is induced. We study the statics and dynamics of the unwrapping process by computer simulations and simple phenomenological theory. We find two different scenarios depending on the chain stiffness: For a flexible chain, the extension of the complex scales linearly with the external force applied. The sphere-chain complex is disordered; i.e., there is no clear winding of the chain around the sphere. For a stiff chain, on the other hand, the complex structure is ordered, which is reminiscent of nucleosome. There is a clear winding number, and the unwrapping process under external stretching is discontinuous with jumps of the distance-force curve. This is associated with discrete unwinding processes of the complex. Our predictions are of relevance for experiments, which measure force-extension curves of DNA-protein complexes, such as nucleosome, using optical tweezers.

UR - http://www.scopus.com/inward/record.url?scp=42749104413&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=42749104413&partnerID=8YFLogxK

U2 - 10.1103/PhysRevE.70.021801

DO - 10.1103/PhysRevE.70.021801

M3 - Article

C2 - 15447507

AN - SCOPUS:42749104413

VL - 70

JO - Physical Review E

JF - Physical Review E

SN - 2470-0045

IS - 2

ER -