T. E. Cheatham III, P. A. Kollman
Department of Medicinal Chemistry, College of Phamacy
University of Utah


Cheatham TE, Kollman PA
Structure 1997 5:1297-1311
Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT](2) in the presence of hexaamminecobalt(III)
Background: Duplex DNA is more than a simple information carrier. The sequence-dependent structure and its inherent deformability, in concert with the subtle modulating effects of the environment, play a crucial role in the regulation and packaging of DNA. Recent advances in force field and simulation methodologies allow molecular dynamics simulations to now represent the specific effects of the environment. An understanding of the environmental dependence of DNA structure gives insight into how histones are able to package DNA, how various proteins are able to bind and modulate nucleic acid structure and will ultimately aid the design of molecules to package DNA for more effective gene therapy.


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