Chemical Probing of tDNA^(Phe) with Transition Metal Complexes: A Structural Comparison of RNA and DNA

The three-dimensional folding of tDNA^(Phe) has been examined and compared to native tRNA^(Phe) using a series of shape-selective transition metal complexes as chemical probes of nucleic acid structure. Rh(phen)_2phi^(3+) (phen = phenanthroline, phi = 9,10-phenanthrenequinonediimine), which targets sites of tertiary interaction in tRNA^(Phe), cleaves specifically at similar sites on tDNA^(Phe). However, this rhodium complex also targets 5'-pyr-pyr-pur-3' sites within the acceptor and anticodon stems of tDNA; Rh(phen)_2phi^(3+)generally targets 5'-pyr-pyr-pur-3' sites in B-form duplex DNA. On tRNA^(Phe), Rh(DIP)_3^(3+) (DIP = 4,7- diphenyl-1,10-phenanthroline) specifically cleaves C70, which neighbors a GU mismatch, and targets ψ55 as well, within the hydrophobic region of tRNA^(Phe). On tDNA^(Phe) no specific cleavage by Rh(DIP)_3^(3+) is observed. The cleavage studies, taken together, indicate that globally the tertiary folding of tDNA^(Phe) resembles that of tRNA^(Phe). However, the double helical regions of the DNA analog differ from tRNA^(Phe), likely in adopting a more B-like conformation. As a consequence, the GT mismatch within the acceptor stem of tDNA does not present the same recognition elements as in tRNA, and the GT mismatch is no longer recognized by the shape-selective rhodium complex. The present work underscores the utility of applying DNA analogs to studies of RNA structure and function, since the general folding characteristics of the two polymers are likely to be similar. However, structural probing with transition metal complexes offers a valuable companion to such experiments, since the shape-selective probes, with sensitivity, may be used to delineate locally on the polymer those regions which may differ in structure