Transfer-matrix calculations of the effects of tension and torque constraints on DNA–protein interactions

@article{Efremov2018TransfermatrixCO,
  title={Transfer-matrix calculations of the effects of tension and torque constraints on DNA–protein interactions},
  author={A. Efremov and Jie Yan},
  journal={Nucleic Acids Research},
  year={2018},
  volume={46},
  pages={6504 - 6527}
}
Abstract Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA… Expand
4 Citations

Figures, Tables, and Topics from this paper

Elasticity as the Basis of Allostery in DNA.
  • 2
  • PDF
DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?
  • 6
The Transfer Matrix Method: Analysis of Nonuniform Multiport Systems
  • 1
  • PDF

References

SHOWING 1-10 OF 213 REFERENCES
Transfer-matrix calculations of DNA polymer micromechanics under tension and torque constraints.
  • 7
  • PDF
Theoretical Methods for Studying DNA Structural Transitions under Applied Mechanical Constraints
  • 1
  • PDF
Effects of DNA-distorting proteins on DNA elastic response.
  • J. Yan, J. Marko
  • Chemistry, Medicine
  • Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2003
  • 83
Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.
  • 4
Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA
  • 63
  • PDF
Intrinsic and force-generated cooperativity in a theory of DNA-bending proteins.
  • H. Zhang, J. Marko
  • Physics, Chemistry
  • Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2010
  • 15
  • PDF
Pulling chromatin fibers: computer simulations of direct physical micromanipulations.
  • 80
Mechanosensing of DNA bending in a single specific protein-DNA complex
  • 17
  • PDF
...
1
2
3
4
5
...