Nucleic major, minor groove

Tris(phenanthroline) complexes of ruthenium(II), cobalt(III), and rhodium(III) are octahedral, substitutionally inert complexes, and as a result of this coordina-tive saturation the complexes bind to double-helical DNA through a mixture of noncovalent interactions. Tris(phenanthroline) metal complexes bind to the double helix both by intercalation in the major groove and through hydrophobic association in the minor groove. " " Intercalation and minor groove-binding are, in fact, the two most common modes of noncovalent association of small molecules with nucleic acids. In addition, as with other small molecules, a nonspecific electrostatic interaction between the cationic complexes and the DNA polyanion serves to stabilize association. Overall binding of the tris(phenanthroline) complexes to DNA is moderate (log K = 4)." ... 

The theoretical basis for such a rationale has been laid in the recent work of Pack et al [161,162]. Using the Poisson-Boltzmann approximation the pH-contour maps on and near the surface of B-DNA ( poly(dG).poly(dC)) have been constructed under simulated conditions of 45 mM tris buffer with 3mM Mg at pH 7.5. Three domains of high ET concentration (>10p.M) are predicted one is spread over the minor groove and two are localised in the major groove near N7(G) and C5(C) for a G.C base pair [114,163]. The reduction in pH by two units would translate into one hundred fold increase in TC production compared to the bulk rate. This is manifested in the accelerated rate of DNA-mediated hydrolysis. Elaborating on the two state model of Islam et al [149] in which the DE is either free or statically bound. Pack and Wong [163(a)] concluded that the catalysis by DNA is primarily an electrostatic effect of acidic domains in the surface grooves of the nucleic acid. While such computations were found satisfactory for a //-BaPDE hydrolysis, they could not adequately reproduce... 

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