Solution Conformation of a Bizelesin A-tract Duplex Adduct: DNA-DNA Cross-linking of an A-tract Straightens Out Bent DNA

The DNA cross-linker bizelesin has been previously shown to form interhelical interstrand cross-links with adenine residues six base-pairs apart (including the modified adenine residues). Sequence specificity studies have shown that the ligand has a high affinity for the intrinsically bent A-tract sequence [d(CGTTTTTCG):d(CGAAAAACG()]. However, gel retardation studies have shown that the cross-linked duplex retains none of the characteristic A-tract bending observed within the unmodified duplex. Two-dimensional¹H-NMR experiments have not only confirmed the sites of cross-linking into the duplex, but have also shown the loss of inherent A-tract characteristics, including reduced crosspeak intensities between the H2s of the central adenine residues and the cross-strand H1′ of the base one base removed to the 3′ side. This observation suggests loss of propeller twisting within these central adenine residues and provides insight into the controversial origin of A-tract bending. This study is important because it validates the use of bizelesin as a probe for determining the importance of A-tract-induced bending in transcriptional and replicational elements.