Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

Crystal structures of B-form DNA have provided insights into the global and local conformational properties of the double helix, the solvent environme nt, drug binding and DNA packing. For example, structures of the duplex wit h sequence CGCGAATTCGCG, the Dickerson-Drew dodecamer (DDD), established a unique geometry of the central A-tract and a hydration spine in the minor g roove. However, our knowledge of the various interaction modes between meta l ions and DNA is very Limited and almost no information exists concerning the origins of the different effects on DNA conformation and packing exerte d by individual metal ions. Crystallization of the DDD duplex in the presence of Mg2+ and Ca2+ yields d ifferent crystal forms. The structures of the new Ca2+-form and isomorphous structures of oligonucleotides with sequences GGCGAATTCGCG and GCGAATTCGCG were determined at a maximum resolution of 1.3 Angstrom. These and the 1.1 Angstrom structure of the DDD Mg2+-form have revealed the most detailed pi cture yet of the ionic environment of B-DNA. In the Mg2+ and Ca2+-forms, du plexes in the crystal lattice are surrounded by 13 magnesium and 11 calcium ions, respectively. Mg2+ and Ca2+ generate different DNA crystal lattices and stabilize differe nt end-to-end overlaps and lateral contacts between duplexes, thus using di fferent strategies for reducing the effective repeat length of the helix to ten base-pairs. Mg2+ crystals allow the two outermost base-pairs at ether end to interact laterally via minor groove H-bonds, turning the 12-mer into an effective 10-mer. Ca2+ crystals, in contrast, unpair the outermost base -pair at each end, converting the helix into a 10-mer that can stack along its axis. This reduction of a 12-mer into a functional 10-mer is followed n o matter what the detailed nature of the 5'-end of the chain: C-G-C-G-A-... , G-G-C-G-A-..., or a truncated G-C-G-A-... Rather than merely mediating cl ose contacts between phosphate groups, ions are at the origin of many well- known features of the DDD duplex structure. A Mg2+ coordinates in the major groove, contributing to kinking of the duplex at one end. While Ca2+ resid es in the minor groove, coordinating to bases via its hydration shell, two magnesium ions are located at the periphery of the minor groove, bridging p hosphate groups from opposite strands and contracting the groove at one bor der of the A-tract. (C) 1999 Academic Press.