Rh(Phen)2Phi3+ as a Shape-Selective Probe of Triple Helices

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Abstract
RNA pur*pur-pyr and pyr*pur-pyr (pur = purine, pyr = pyrimidine) triple helices consisting of a Watson-Crick base-paired 28mer hairpin duplex and a Hoogsteen base-paired purine or pyrimidine 12mer are targeted with photoactivated cleavage by the metal complex Rh(phen)2phi3+ (phen = phenanthroline, phi = 9, 10-phenanthrenequinone diimine). The metal complex interacts with these triple helices in a structure-specific manner. Different cleavage patterns are seen with the pyr*pur-pyr and pur*pur-pyr motifs. Cleavage is seen on both of the Watson-Crick strands of the former motif and primarily on the purine Watson-Crick strand of the latter motif. Little cleavage is seen on the Hoogsteen strand for either motif. Importantly, the metal complex shows no detectable cleavage on the A-form RNA duplex in the absence of the third Hoogsteen strand. The cleavage patterns are consistent with an intercalated model for the metal complex in the triple helix. Similar cleavage is seen on DNA triple helices, but over a background of duplex cleavage. Targeting of synthetic RNA triple helices, but not duplex regions, by Rh(phen)2phi3+ provides a basis for the chemical probing of triply bonded sites in folded RNA molecules.