Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation.
AUTOR(ES)
Subramanian, P S
RESUMO
A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo computer simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG).d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indicative of discrete solvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 4359-4363] for both A.T and C.G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=279875Documentos Relacionados
- Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove.
- Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width.
- Fluorescent d(CGCGAATTCGCG): characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate.
- The role of a minor groove spine of hydration in stabilizing poly(dA).poly(dT) against fluctuational interbase H-bond disruption in the premelting temperature regime.
- How the transition frequencies of microtubule dynamic instability (nucleation, catastrophe, and rescue) regulate microtubule dynamics in interphase and mitosis: analysis using a Monte Carlo computer simulation.