Electrostatic interactions nucleic acid-metal binding

For many metal ions, the initial electrostatic interaction can be followed by stronger and more specific binding with nucleic acids via the formation of outer- and inner-sphere complexes. The formation of such complexes may be strongly accelerated (in comparison to binding to nucleosides and nucleotides) because of the polyelecfrolyte effect. 

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)." ... 

One of the most important aspects of the interaction between metals and polynucleotides is that which leads to compactness of structure in the polynucleotides. As polyions, they exhibit structures in solution which are strongly dependent on the concentration and valence of the cations (typically, the compact native structures are favoured by high salt concentrations and particularly by bivalent ions), but even with the transfer RNAs (among the most widely studied nucleic acids and despite analysis of the X-ray structures) the role and location of bound bivalent cations are uncertain. Leroy et al. have used various physical techniques to explore the structure of the central region in a couple of tRNAs from E. coli and thereby obtain evidence on the binding of Mn + and other metal ions. Their interpretation is that simple manganese-phosphate binding is supplemented by electrostatic interaction with distant phosphates. 

Ions are an important component in many chemical and biological systems. Nearly half of all proteins contain metal ions, and they play essential roles in many fundamental biological functions. Some metal ions are critical for both protein structure and function. In enzymes, ions can bind and orient the substrates through electrostatic interactions at the active sites, thus controlling catalytic reaction. Divalent ions are vital in nucleic acid structures. Modeling ion-water and ion-biomolecule interactions accurately is very important. 

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