Nucleic acids coordination modes

More traditional applications of internal coordinates, notably normal mode analysis and MC calculations, are considered elsewhere in this book. In the recent literature there are excellent discussions of specific applications of internal coordinates, notably in studies of protein folding [4] and energy minimization of nucleic acids [5]. 

Table 1. Summary of observed coordination modes for fragments of nucleic acids and derivatives with respect to Pt(II). For numbering of the nucleobases the reader is referred to Fig. 9...

Coordination Complexes and Nucleic Acids. Perspectives on Electron Transfer, Binding Mode, and Cooperativity... 

It is conceivable that an interstrand complex can be created by coordination of a metal ion to the 2PA situated on the PNA or LNA strand and to a nucleobase or phosphodiester group from the opposite, non-modified DNA strand in the nucleic acid duplex. Molecular modeling of LNA DNA duplexes showed that a [3 -I-1] 2PA-M -P04R2 coordination mode can be realized by coordination of a 2PA ligand from one strand and a phosphodiester from either the same strand or from the opposite strand of the LNA DNA duplex (121). This model was supported by data obtained for 2PA-modified PNA DNA duplexes showing that (a) the... 

In this chapter we first summarize the basics needed to consider the interactions of metal ions and complexes with nucleic acids. What are the structures of nucleic acids What is the basic repertoire of modes of association and chemical reactions that occur between coordination complexes and polynucleotides We then consider in some detail the interaction of a simple family of coordination complexes, the tris(phenanthroline) metal complexes, with DNA and RNA to illustrate the techniques, questions, and applications of metal/nucleic-acid chemistry that are currently being explored. In this section, the focus on tris(phenanthroline) complexes serves as a springboard to compare and contrast studies of other, more intricately designed transition-metal complexes (in the next section) with nucleic acids. Last we consider how Nature uses metal ions and complexes in carrying out nucleic-acid chemistry. Here the principles, techniques, and fundamental coordination chemistry of metals with nucleic acids provide the foundation for our current understanding of how these fascinating and complex bioinorganic systems may function. 

Now we may examine in detail the interaction of one class of metal complexes with nucleic acids, how these complexes bind to polynucleotides, the techniques used to explore these binding interactions, and various applications of the complexes to probe biological structure and function. Tris(phenanthroline) metal complexes represent quite simple, well-defined examples of coordination complexes that associate with nucleic acids. Their examination should offer a useful illustration of the range of binding modes, reactivity, techniques for study, and applications that are currently being exploited and explored. In addition, we may contrast these interactions with those of other transition-metal complexes, both derivatives of the tris(phenanthroline) family and also some complexes that differ substantially in structure or reactivity. 

Many recents studies have focused on applications of metallointerca-lation, which is also an important noncovalent interaction of metal complexes with nucleic acids. Intercalation is a common mode of association of small molecules with DNA, where a flat aromatic heterocyclic moiety inserts and stacks in between the DNA base pairs (13). Lippard and coworkers (14) determined in 1974 that platinum(II) complexes containing an aromatic heterocyclic ligand such as terpyridine could intercalate in DNA. Figure 2c shows such a stacking interaction of such a complex in a dinucleotide (15). Recently, we have found that intercalation is not restricted to completely flat, square planar complexes, but partial intercalation of ligands coordinated to octahedral metal centers is feasible as well... 

The Pt anticancer agents and other potential therapeutic properties drive interest in complexes of these nonbiological metals with nucleic acids. In addition to standard nucleobase coordination modes, the heavy metals can facilitate deprotonation of and bind to exocyclic amino groups. Coordination compounds of Ru, Rh, and Re have been used in the study of... 

---