The cleavage reaction is nonetheless remarkably

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The cleavage reaction is nonetheless remarkably sequence-neutral and therefore shows some promise for photofootprinting applications. In fact, the applicability of uranyl acetate typifies how simple coordination chemistry and now even pho- tochemistry may be helpful in the design of a variety of reagents that interact and cleave DNA, both nonspecifically and specifically. The biochemical tech- niques used to monitor such processes are sufficiently sensitive that even quite inefficient reactions in solution can be harnessed in developing useful reagents. The better our understanding of the chemistry of the coordination complex, the more effectively it may be utilized. The best derivative of a tris(phenanthroline) metal complex currently being applied in footprinting experiments is Rh(phi)zbpy3+, a second-generation de- rivative of the tris(phenanthroline) series 67 that binds DNA avidly by intercala- tion and in the presence of light promotes direct strand cleavage by hydrogen- atom abstraction at the C3'-position on the sugar. 31 Since no diffusing interme- diate is involved in this photocleavage reaction, the resolution of the footprint- ing pattern is to a single nucleotide. Here the excited-state transition-metal chemistry involves a ligand-to-metal charge transfer, producing a phi cation rad- ical that directly abstracts the hydrogen from the sugar at the intercalated site. The high efficiency of this photoreaction and high sequence-neutral binding of the complex to double-stranded DNA add to the utility of this reagent in foot- printing studies. Indeed, both DNA-binding proteins, bound in the major groove, and small natural products, associated with the minor groove, have been foot- printed with Rh(phi)zbpy 3 + to precisely that size expected based upon crystal- lographic results. One may hope that this and other photofootprinting reagents will soon find applications for footprinting experiments in vivo.
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484 8 I METAUNUCLEIC-ACID INTERACTIONS C. Conformational Probes Metal complexes are also finding wide application in probing the local variations in conformation that arise along nucleic-acid polymers. X-ray crystallography has been critical in establishing the basic conformational families of double- helical DNA, and to some extent how conformations might vary as a function of nucleic-acid sequence. Yet many conformations have still not been described to high resolution, and only a few oligonucleotides have been crystallized. Other techniques are therefore required to bridge the small set of oligonucleotide crys- tal structures that point to plausible structures and the large array of structures that arise as a function of sequence on long helical polymers. Furthermore, only a very small number of RNA polymers has been characterized crystallographi- cally; hence other chemical methods have been needed to describe the folding patterns in these important biopolymers. Metal complexes, mainly through spe- cific noncovalent interactions, appear to be uniquely useful in probing the struc- tural variations in nucleic acids.
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