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Nucleic Acids Research, 2002, Vol. 30, No. 16 3615-3623
© 2002 Oxford University Press

Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies

Donald Hamelberg, Loren Dean Williams1 and W. David Wilson*

Department of Chemistry, Georgia State University, 50 Decatur Street, Atlanta, GA 30303, USA and 1 School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA

*To whom correspondence should be addressed. Tel: +1 404 651 3903; Fax: +1 404 651 2751; Email: chewdw{at}panther.gsu.edu
Correspondence may also be addressed to Loren Dean Williams. Tel: +1 404 894 9752; Fax: +1 404 894 7452; Email: loren.williams{at}chemistry.gatech.edu

Alternative models have been presented to provide explanations for the sequence-dependent variation of the DNA minor groove width. In a structural model groove narrowing in A-tracts results from direct, short-range interactions among DNA bases. In an electrostatic model, the narrow minor groove of A-tracts is proposed to respond to sequence-dependent localization of water and cations. Molecular dynamics simulations on partially methylphosphonate substituted helical chains of d(TATAGGCCTATA) and d(CGCGAATTCGCG) duplexes have been carried out to help evaluate the effects of neutralizing DNA phosphate groups on the minor groove width. The results show that the time-average minor groove width of the GGCC duplex becomes significantly more narrow on neutralizing the phosphate backbone with methylphosphonates. The minor groove of the AATT sequence is normally narrow and the methylphosphonate substitutions have a smaller but measurable affect on this sequence. These results and models provide a system that can be tested by experiment and they support the hypothesis that the electrostatic environment around the minor groove affects the groove width in a sequence-dependent dynamic and time-average manner.


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