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.
Version of Record
Abstract
Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)10·d(A)10·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