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A 2'-deoxyuridylate dimer cyclized via cross-linkage by an ethylene (U(et)(p)U) or a propylene (U(pr)(p)U) linker at the 5-position was incorporated into DNA oligomers. Fluorescence resonance energy transfer (FRET) experiments showed that they bent at approximately 90 degrees . We investigated binding abilities of U(et)(p)U and U(pr)(p)U DNA oligomers to HMGB1 A-box protein, which specifically binds to bent DNA, using nuclear magnetic resonance (NMR) spectroscopy. Both DNA oligomers bind to HMGB1 A-box protein, however, the U(et)(p)U DNA oligomer has higher affinity than the U(pr)(p)U DNA oligomer. In order to explain this difference, we studied the solution structures of the U(et)(p)U and U(pr)(p)U DNA oligomers using NMR. Most (1)H signals except for 4', 5' and 5'' were assigned. Cross-peak patterns of (1)H-(1)H NOESY spectra indicate that both oligomers have right-handed B-form like structures and the cyclization in 2'-deoxyuridylates does not break Watson-Crick base pairs. Chemical shift differences between these two DNA oligomers suggest the presence of the local structural differences in the region of 2'-deoxyuridylate dimer and its 3' side between the U(et)(p)U and U(pr)(p)U DNA oligomers.

NMR studies of DNA recognition mechanism of HMGB1 protein