Title

Molecular Dynamics Simulations of the d(T·A·T) Triple Helix

ACS Citation

Shields, G. C.; Laughton, C. A.; Orozco, M. Molecular Dynamics Simulations of the d(T-·A-·T) Triple Helix. J. Am. Chem. Soc. 1997, 119 (32), 7463-€“7469.

Abstract

Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)10{\textperiodcentered}d(A)10{\textperiodcentered}d(T)10. The structures sampled during the trajectory resemble closely the B-type model for the DNA triplex proposed on the basis of NMR data, although there are some subtle differences. Alternative P- and A-type conformations for the triplex, suggested from X-ray experiments, are not predicted to contribute significantly to the structure of the DNA triplex in solution. Comparison with the best available experimental data supports the correctnes of the MD-generated structures. The analysis of the collected data gives a detailed picture of the characteristics of triple-helix DNA. A new and interesting pattern of hydration, specific for triplex DNA, is an important observation. The results suggest that molecular dynamics can be useful for the study of novel nucleic acid structures.

Source Name

Journal of the American Chemical Society

Publication Date

1997

Volume

119

Issue

32

Page(s)

7463-7469

Document Type

Citation

Citation Type

Article