Electrochemical sensors: Taking charge of detection.

ruthenium complexes and DNA. Jacqueline Barton and co-workers2 co-crystallized Δ-[Ru(bpy)2(dppz)] with the 12-mer DNA sequence d(CGGAAATTACCG) — a self-complementary double helix with two adenine:adenine (A:A) mismatches. An atomic-resolution structure analysis of the resulting co-crystal revealed a complex pattern of interactions between the ruthenium compound and the DNA. Five individual ruthenium compounds are bound to each duplex, all from the minor groove direction. Intercalation between base pairs occurs at both normal sites and mismatched A:A ones, where the binding ejects both adenosines (Fig. 1a). The [Ru(bpy)2(dppz)] complexes are perfectly positioned so that each flipped-out adenine base is neatly stacked between a pair of 2,2′-bipyridines, and thus stabilized. The net effect is a pattern of bipyridine–adenine interactions that effectively extends along the complete length of the minor groove in this 12-mer duplex. It is tempting to suggest that the enhanced luminescence observed on binding at the mismatched sites is in part due to the extended bipyridine–adenine extra-helical stacking. The minor-groove directionality contrasts with that inferred previously by this group using NMR and fluorescence measurements, and it is also tempting to speculate, as do Barton and co-workers, that this suggests a delicate balance between major and minor groove intercalation. However, this change from major to minor is not really so strange given the flipping-out of the adenine bases results in a narrowing of the minor groove, and in turn in close contact between the complex and the groove walls. It is difficult to envisage these occurring to the same extent in the much wider major groove. The two crystal structures determined by Christine Cardin and colleagues3 involve the Λ-[Ru(phen)2(dppz)] complex bound to two 10-mer duplexes, both free of any mispairing. One sequence is d(CCGGTACCGG), and the other has the central two nucleotides reversed to be AT (d(CCGGATCCGG)). For the TA-centred duplex (Fig. 1b), three bound ruthenium complexes are observed that adopt distinct modes of intercalation. One complex is symmetrically intercalated at the central TA step of this sequence, which is clearly a preferred binding site — there is no bound complex at the corresponding AT step in the reversed sequence. In this crystal, the ruthenium compound also binds to the minor groove — a preference that can at first sight be surprising. In the structure by Barton et al. discussed above2, the driving force for [Ru(bpy)2(dppz)] to bind through the minor groove is presumed to arise from the extra-helical stacking. Extrapolation might have suggested that the absence of mismatches could lead to major groove binding instead. Yet, the [Ru(phen)2(dppz)] complex of Cardin et al. has phenanthroline rather than bipyridine groups; these are somewhat larger and fit very snugly against the walls of the minor groove in a way that would not occur in the major groove. Thus, again, the arrangement is not so strange. It is tantalizing to speculate that the smaller bipyridine groups in the [Ru(bpy)2(dppz)] complex might well drive the equilibrium towards the major groove. However, we must await further crystal structures of a range of DNA sequences, with other enantiomers of these complexes and ultimately on DNA in chromatin — DNA–protein nanostructure found in cells — for more definitive biologically relevant answers to the major versus minor groove question. ❐