Conformational flexibility of B-DNA at 0.74 angstrom resolution: d(CCAGTACTGG)(2)

The affinity and specificity of a Ligand for its DNA site is a function of the conformational changes between the isolated and complexed states. Altho ugh the structures of a hydroxypyrrole-imidazole-pyrrole polyamide dimer wi th 5'-CCAGTACTGG-3' and the frp repressor recognizing the sequence 5'-GTACT -3' are known, the baseline conformation of the DNA site would contribute t o our understanding of DNA recognition by these ligands. The 0.74 Angstrom resolution structure of a B-DNA double helix, 5'-CCAGTACTGG-3', has been de termined by X-ray crystallography. Six of the nine phosphates, two of four bound calcium ions and networks of water molecules hydrating the oligonucle otide have alternate conformations. By contrast, nine of the ten bases have a single, unique conformation with hydrogen atoms visible in most cases. T he polyamide molecules alter the geometry of the phosphodiester backbone, a nd the water molecules mediating contacts in the trp repressor/operator com plex are conserved in the unliganded DNA. Furthermore, the multiple conform ational states, ions and hydration revealed by this ultrahigh resolution st ructure of a B-form oligonucleotide are potentially general considerations for understanding DNA-binding affinity and specificity by ligands. (C) 2000 Academic Press.