Metal ions nucleic acid

Interactions of the same water molecules with RNA nucleotides (via H-bonding) and metal ions (via inner-sphere coordination) could stabilize specific metal ion-nucleic acid complexes (e.g. in Mg + -tRNA chelates) and also create the possibility for direct proton transfer through a water chain that could play a role in ribozyme-metal ion catalysis and in the mechanism of metal-dependent nucleases and polymerases. Similar types of H-bonds between different nucleotide residues have been found in tRNA tertiary structures, where they provide additional stabilization of tertiary interactions. 

X-ray crystallographic analyses usually provide structural information that correctly represents the actual structures of metal ion-nucleic acid complexes in the crystal this usually represents an environment that is drastically different from normal solution conditions. Obviously, such analyses are limited to complexes that are both stable and amenable to crystallization. In comparison, solution NMR spectroscopy data are much more generally applicable to the analysis of metal ion-nucleic acid structure, " " but can be more easily misinterpreted owing to factors such as the distribution of metal ions among several binding sites and the intrinsically weaker nature of some of the interactions that are studied. Also, nucleic acid crystallization requires the formation of ordered and uniform intermolecular interactions between nucleic acids. These intermolecular interactions may either compete or interfere with the formation of certain metal-nucleic complexes and promote the formation of unnatural metal binding centers. ... 

This article does not attempt to be comprehensive, but rather presents selected examples to illustrate key facets of metal ion-nucleic acid interaction. The focus is on the chemical and structural properties of nucleic acids and metal ions relevant to their interactions, and in illustrating that both contribute as equal partners to the complexity of their interactions. 

Toxicity and Metal-related Diseases of Genetic Origin). There are only a few processes for which it is clear that the nucleic acid is the primary target of metal action.In most cases, it is not clear whether the observed effects actually result from direct metal ion-nucleic acid interaction, since other species, such as specific proteins see Zinc DNA-binding Protein, may be mediators between the metal ion and the nucleic acid in these processes in To better understand... 

D. J. Earnshaw and M. J. Gait, Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions, Nucleic Acids Res., 26 (1998) 5551-5561. 

As already noted, metal ions play a vital role in DNA tetraplex structures. The first MD study that did address this point was published in 1994. It was found that the simulation could reproduce a few properties of the structure but could not correctly describe the metal ion nucleic acid interaction. This is not surprising as at that time the particle-mesh Ewald roach was not yet available. Later simulations do not suffer from this deficioicy. 

Ternary Metal Ion-Nucleic Acid Base-Protein Complexes Michal Sabat... 

Zivarts M, Liu Y, Breaker RR Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res 2005, 33(2) 622—631. 

L. G. Marzilli, T. J. Kistenmacher, and G. L. Eichhom Structural Principles of Metal Ion—Nucleotide and Metal Ion—Nucleic Acid Interactions (Reference 8, pp. 179— 250). 

Metal ion Nucleic acid (%GC) IgK (n) IgKi igK2 AG Experimental ( i) ( 2) [kcalmoP ] method Conditions, comments Ref... 

One of the important questions in metal ion-nucleic acid coordination is to find out to what extent neighboring nucleotide units affect binding of a metal ion at a given site [58]. Some answers to this question can be found by studying ligands of the... 

Cbaracterization of Metal Ion-Nucleic Acid Interactions in Solution... 

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