• Cite Icon77
  • https://doi.org/10.1146/annurev.bioeng.6.062403.132016Copy DOI Icon

DNA Mechanics

Show More
  • Abstract
  • Literature Map
  • References
  • Citations
  • Similar Papers
Abstract

We review the history of DNA mechanics and its analysis. We evaluate several methods to analyze the structures of superhelical DNA molecules, each predicated on the assumption that DNA can be modeled with reasonable accuracy as an extended, linearly elastic polymer. Three main approaches are considered: mechanical equilibrium methods, which seek to compute minimum energy conformations of topologically constrained molecules; statistical mechanical methods, which seek to compute the Boltzmann distribution of equilibrium conformations that arise in a finite temperature environment; and dynamic methods, which seek to compute deterministic trajectories of the helix axis by solving equations of motion. When these methods include forces of self-contact, which prevent strand passage and preserve the topological constraint, each predicts plectonemically interwound structures. On the other hand, the extent to which these mechanical methods reliably predict energetic and thermodynamic properties of superhelical molecules is limited, in part because of their inability to account explicitly for interactions involving solvent. Monte Carlo methods predict the entropy associated with supercoiling to be negative, in conflict with a body of experimental evidence that finds it is large and positive, as would be the case if superhelical deformations significantly disrupt the ordering of ambient solvent molecules. This suggests that the large-scale conformational properties predicted by elastomechanical models are not the only ones determining the energetics and thermodynamics of supercoiling. Moreover, because all such models that preserve the topological constraint correctly predict plectonemic interwinding, despite these and other limitations, this constraint evidently dominates energetic and thermodynamic factors in determining supercoil geometry. Therefore, agreement between predicted structures and structures obtained experimentally, for example, by electron microscopy, does not in itself provide evidence for the correctness or completeness of any given model of DNA mechanics.

Similar Papers
  • Research Article
  • Citations18

Realization of sub 1 V polymeric EO modulators through systematic definition of material structure/function relationships

  • Oct 01, 2001
  • Synthetic Metals
  • Larry R Dalton
  • Research Article
  • Citations14

Comparison of mechanical and chemomechanical methods of caries removal in deciduous and permanent teeth: A SEM study

  • Jan 01, 2012
  • Journal of Indian Society of Pedodontics and Preventive Dentistry
  • A Avinash +5
  • Research Article
  • Citations8

Pressure effects on thermo-mechanical properties of intermetallic B2-type FeAl alloy

  • Jan 01, 2020
  • The European Physical Journal B
  • Nguyen Viet Tuyen +5
  • Research Article
  • Citations1

Using dynamic methods for compaction of particulate composite materials

  • Sep 01, 2003
  • Journal de Physique IV (Proceedings)
  • V Popov +4
  • Research Article
  • Citations16

Thermodynamic properties of the normal alcohols, C1 C12

  • Oct 01, 1961
  • Journal of Applied Chemistry
  • J H S Green
  • Book Chapter
  • Citations10

Quantum Field Theoretical Methods in Statistical Mechanics

  • Jan 01, 1991
  • Ryogo Kubo +2
  • Research Article
  • Citations7

On the application of statistical mechanics to the general dynamics of matter and ether

  • Jul 10, 1905
  • Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character
  • James Jeans
  • Research Article
  • Citations38

Thermodynamics of nuclei in thermal contact

  • Jan 28, 2011
  • Physical Review C
  • Karl-Heinz Schmidt +1
  • Research Article
  • Citations22

Stratification as a general variance reduction method for Markov chain Monte Carlo.

  • Jan 01, 2020
  • SIAM/ASA Journal on Uncertainty Quantification
  • Aaron R Dinner +3
  • Research Article

Fannes, M.; Verbeure, A. (eds.), Mathematical Methods in Statistical Mechanics. Conference Proceedings, Leuven, 23–24 June 1988. Leuven, Leuven University Press 1989. III, 196 pp., Bef 600.‐. ISBN 90–6186–306‐6 (Leuven Notes in Mathematical and Theoretical Physics. Vol. 1. Ser. A: Mathematical Physics)

  • Jan 01, 1991
  • ZAMM - Journal of Applied Mathematics and Mechanics / Zeitschrift für Angewandte Mathematik und Mechanik
  • P Möbius
  • Research Article
  • Citations4

Structural and Thermomechanical Properties of Zincblende-Type ZnX (X = S, Se, Te)

  • Jun 21, 2019
  • Journal of Electronic Materials
  • Ho Khac Hieu +6
  • Research Article
  • Citations68

Pyrrole: chemical thermodynamic properties

  • Jun 01, 1967
  • The Journal of Physical Chemistry
  • Donald William Scott +8
  • Research Article
  • Citations30

The statistical mechanical theory of water transport through unsaturated soil: 1. The conservation laws

  • Jun 01, 1978
  • Water Resources Research
  • Garrison Sposito
  • Research Article
  • Citations216

The Green function method in statistical mechanics: Bonch-Bruevich and Tyablikov (North-Holland Publishing Co., Amsterdam, 1962. v-251 p. 27.50 fl.)

  • Oct 01, 1962
  • Nuclear Physics
  • L.R
  • Research Article

The Kinetic Theory of Transport Processes in Turbulent Media of Moderate Density

  • Dec 01, 1999
  • Annals of the New York Academy of Sciences
  • Emir G Aznakaev
Cactus Communications logo

Copyright 2026 Cactus Communications. All rights reserved.