NMR structural study of DNA oligomers containing alkylene crosslinked cyclic 2'-deoxyuridylate dimers

A 2'-deoxyuridylate dimer cyclized via cross-linkage by ethylene (U(et)(p)U) or propylene (U(pr)(p)U) linker was incorporated in DNA oligomer. Fluorescence resonance energy transfer (FRET) experiment showed that they bent at a sharp angle of approximately 90 degree. HMGB1 A-box protein, which selectively binds to bent DNA, binds to the U(et)(p)U DNA oligomer with high affinity, but not to the U(pr)(p)U. In order to explain this difference, we have 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 by (1)H-(1)H two-dimensional NMR spectra and natural abundance (1)H-(13)C HSQC spectra. Cross-peak patterns of (1)H-(1)H NOESY spectra indicate that both oligomers have right-handed B-form DNA like structures and the cyclization in 2'-deoxyuridylates by alkylene crosslinking does not break Watson-Crick base pairs. Chemical shift differences between these two DNA oligomers are localized to the region of 2'-deoxyuridylate dimer and its 3' side. These chemical shift differences and some characteristic NOE crosspeaks suggest the presence of the local structural differences in these regions between the U(et)(p)U and U(pr)(p)U DNA oligomers.