Photoadduct leading to crosslinking in Ru(II)-derivatized oligonucleotides

Cobalt(III)hexaammine-dependent photocrosslinks in the hairpin ribozyme

We have utilized the hairpin ribozyme, an RNA enzyme whose structure has been solved by high-resolution methods, to develop a new tool for mapping nucleobase-stacking interactions and potential metal-binding sites in RNA molecules. This tool involves the photoactivation of a specifically bound cobalt(III)hexaammine molecule at wavelengths corresponding to excitation of the metal ion complex only; no base excitation is involved. The photoexcitation initiates a process which strongly promotes the formation of a novel covalent bond or crosslink between one base (termed the "first base"), which is close in space to the excited cobalt(III)hexaammine complex, and another base upon which the first base is closely stacked. These crosslinked species can be isolated and sequenced; their activities can be analyzed to ensure that the crosslinked structures represent an active conformation of the molecule. We have shown that, as in electron transfer in DNA, several criteria must be met to result in the successful formation of these crosslinks. These include the appropriate oxidation potential of the first donor base, the stacking and close interaction of the two donor bases involved in the crosslink, and the binding of a specific cobalt(III)hexaammine molecule to the first donor base. Additionally, we have determined that this crosslinking is pH-sensitive, although the cause of this sensitivity remains unknown. This tool has proven useful in the past for the analysis of the hairpin ribozyme folded structure, and has been applied to identify potential metal-binding sites on the hairpin and extended hammerhead ribozymes.

Detection of secondary structures in 17-mer Ru(II)-labeled single-stranded oligonucleotides from luminescence lifetime studies

The emission properties of a non intercalating complex, [Ru(TAP)2(dip)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene; dip = 4,7-diphenyl-1,10-phenanthroline), tethered to 17-mer single-stranded oligodeoxyribonucleotides (ODNs) either in the middle or at the 5'-end of the sequence, are determined. The results highlight the fact that the luminescence of this metallic compound is sufficiently sensitive to its microenvironment to probe self-structuration of these short single-stranded ODNs. It is shown that the weighted averaged emission lifetimes (tau(M)) along with the quenching rate constants of luminescence by oxygen reflect particularly well different structures adopted by the different ODNs sequences. The determination of these parameters thus offers an elegant way to examine possible structurations of synthetic single-stranded ODNs that play important roles in biological applications.