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

ABSTRACT: 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 methy

SUBMITTER: Hamelberg D 

PROVIDER: S-EPMC134239 | biostudies-literature | 2002 Aug

REPOSITORIES: biostudies-literature