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Science 21 August 1992:
Vol. 257. no. 5073, pp. 1110 - 1115
DOI: 10.1126/science.257.5073.1110
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Articles

Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA

Tamar Schlick 1 and Wilma K. Olson 2

1 Chemistry Department and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012
2 Department of Chemistry, Rutgers, State University of New Jersey, Wright-Rieman Laboratories, New Brunswick, NJ 08903

Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement analytical models and experimental data. Through association of an energy function, minimum-energy supercoiled conformations,fluctuations about these states, and interconversions among forms may be sought. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be associated with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/ implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.
J. Arsuaga, M. Vazquez, S. Trigueros, D. W. Sumners, and J. Roca (2002)
PNAS 99, 5373-5377
   Abstract »    Full Text »    PDF »
Knotting of a DNA chain during ring closure.
S. Shaw and J. Wang (1993)
Science 260, 533-536
   Abstract »    PDF »


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Science. ISSN 0036-8075 (print), 1095-9203 (online)