HAIRPINS IN A DNA SITE FOR TOPOISOMERASE-II STUDIED BY H-1-NMR AND P-31-NMR

H-1- and P-31-NMR and UV-absorption studies were carried out with the oligonucleotide strands d(AGCT-TATC-ATC-GATAAGCT) (-ATC-) and d(AGCTTA TC-GAT-GATAAGCT) (-GAT-) contained in the strongest and salt resistant cleavage site for topoisomerase II in pBR322 DNA. We found that the t wo oligonucleotides were stabilized under a hairpin structure characte rized by a eight base pair stem and a three base loop at low DNA and s alt concentrations. In such experimental conditions, only the -GAT- ol igonucleotide displayed a partial homoduplex structure in slow equilib rium with its folded structure. Temperature dependencies of imino prot ons showed that the partial homoduplex of -GAT- melted at a lower temp erature than the hairpin structure. It was suggested that the appearan ce of the partial homoduplex in -GAT- is related to the formation of t wo stabilizing (G-T) mismatched base pairs in the central loop of this structure. Finally, it was inferred from the dispersion of chemical s hifts in the P-31-NMR spectra that the distortions affecting the backb one of the hairpin loop are larger in the case of -ATC-compared with - GAT-. At the same time NOEs proved that the base stacking was stronger within the loop of the -ATC-hairpin.