Bases, metal ions binding

One approach, pursued by two groups in particular, is to use model nucleobases that feature an additional metal-ion binding group. Gokel and co-workers have used this strategy with aza-crown derivatives (50,51). X-ray crystallography of 6is-(3-(l-thyminyl)propyl)-4,13-diaza-18-crown-6, 4, reveals the Na+ is coordinated by T-02 [Na-0 distances 2.488 and 2.468 Al (51). Aza-crown derivatives with multiple base substi-... 

A series of amine-tethered nucleobases such as 8 has also been developed. These ligand systems have allowed the interaction of d-block metal ions with the N3pUrine site to be probed and an indication of base-specific metal-ion binding has begun to emerge (55-58). 

Of all the known sites for metal-ion binding to the heteroatoms of DNA bases, G-N3 is the most elusive. The adjacent 2-amino group is often considered to offer steric hindrance to binding at this site. However, while this undoubtedly influences the chemistry it does not preclude binding. The tri-metalated [ [Pt(N]3(9-Et G N1,N3,N7)]5 compound has for many years been the only structurally characterized example of an N3-coordinated guanine (66). A second example has now been reported, the tetranuclear octacation 16 (56). In this complex both the N7 and N3 atoms are bound to Pd2+ (Fig. 22). The molecule presents an interesting new architecture for a guanine-tetramer. Such structures are well known in DNA chemistry and are almost inevitably metal-ion stabilized (67,68). 

We now look at the values of the free M concentration and hence to the binding strength to selected A synthesised in the cell. The constants are closely common to all cells in their common compartment, their cytoplasm. The values, suited to metabolism, can be put in series in which Na+ and K+ bind poorly and only to a few of the weakest donors based on neutral O-donor centres while other metal ions bind more strongly to O, N and S donors of proteins or small organic molecules in a well-recognised order, i.e. in the Irving/Williams series (see Section 2.17) ... 

Table XIX contains stability constants for complexes of Ca2+ and of several other M2+ ions with a selection of phosphonate and nucleotide ligands (681,687-695). There is considerably more published information, especially on ATP (and, to a lesser extent, ADP and AMP) complexes at various pHs, ionic strengths, and temperatures (229,696,697), and on phosphonates (688) and bisphosphonates (688,698). The metal-ion binding properties of cytidine have been considered in detail in relation to stability constant determinations for its Ca2+ complex and complexes of seven other M2+ cations (232), and for ternary M21 -cytidine-amino acid and -oxalate complexes (699). Stability constant data for Ca2+ complexes of the nucleosides cytidine and uridine, the nucleoside bases adenine, cytosine, uracil, and thymine, and the 5 -monophosphates of adenosine, cytidine, thymidine, and uridine, have been listed along with values for analogous complexes of a wide range of other metal ions (700). Unfortunately comparisons are sometimes precluded by significant differences in experimental conditions.

The availability of different metal ion binding sites in 9-substituted purine and pyrimidine nucleobases and their model compounds has been recently reviewed by Lippert [7]. The distribution of metal ions between various donor atoms depends on the basicity of the donor atom, steric factors, interligand interactions, and on the nature of the metal. Under appropriate reaction conditions most of the heteroatoms in purine and pyrimidine moieties are capable of binding Pt(II) or Pt(IV) [7]. In addition, platinum binding also to the carbon atoms (e.g. to C5 in 1,3-dimethyluracil) has been established [22]. However, the strong preference of platinum coordination to the N7 and N1 sites in purine bases and to the N3 site in pyrimidine bases cannot completely be explained by the negative molecular electrostatic potential associated with these sites [23], Other factors, such as kinetics of various binding modes and steric factors, appear to play an important role in the complexation reactions of platinum compounds. 

As was pointed out in the previous chapter, biologically important metal ions and their ligands can be classified according to the hard-soft theory of acids and bases (Table 2.1). While there are exceptions, most metal ions bind to donor ligands as a function of preferences based on this concept, with hard acids (metal ions) binding preferentially to hard bases (ligands) and soft acids to soft bases. 

Fig. 4A The mechanism of cleavage by ribonuclease A. Two imidazole residues function as general acid-base catalysts. B The single-metal-ion mechanism proposed for cleavage by the hammerhead ribozyme. One metal ion binds directly to the pro-Rp oxygen and functions as a general base catalyst. C The double-metal-ion mechanism proposed for cleavage by the hammerhead ribozyme. Two metal ions bind directly to the 2 -oxygen and the 5 -oxygen...

Because metal ions bind to and modify the reactivity and structure of enzymes and substrates, a wide spectrum of techniques has been developed to examine the nature of metal ions which serve as templates, redox-active cofactors, Lewis acids/bases, ion-complexing agents, etc. 

Metal ions can attach themselves at two different types of sites on a polynucleotide—i.e., the phosphate and the donor groups on the bases. Some of the metal ions do indeed bind at one site, and some metal ions at the other. Those binding to the phosphate will promote the cleavage of the phosphate bond, whereas metal ions binding on the base will inhibit such cleavage in a manner that illustrates one of Dr. Jones points very well. 

Reactions with electrophilic reagents. Reactions of nucleic acids with the simplest electrophile, the proton, have been considered in Section A2. Somewhat similar are the reactions by which metal ions bind at many sites on both the bases and the phosphate groups of the backbone.550... 

Metal ion binding to (133) is quite strong and saturation kinetics occur at low metal ion concentrations presumably leading to complexes of type (134). Base hydrolysis of the Cu11 complex is observed, but attack by both H20 and OH occurs with the Ni11, Co11 and Zn11 complexes. Rate enhancements of > 102 occur for water attack. 

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