Volume 6, Issue 7, Pages 849-861 (July 1998) A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 å resolution  William Shepard, William BT Cruse, Roger Fourme, Eric de la Fortelle, Thierry Prangé  Structure  Volume 6, Issue 7, Pages 849-861 (July 1998) DOI: 10.1016/S0969-2126(98)00087-2

Figure 1 The zipper-like motif in DNA. (a) The initial experimental electron-density map at 2.35 å resolution with the final model superimposed. Contouring is at 2σ above the mean density level. The region shown is the central part of the intercalating adenines. The symmetry-related molecule (in red) is shown to illustrate how the zipper-like dimer is built. (b) Schematic diagram of the base-stacking arrangement in the extended/stretched duplex (the helix is represented unwound). The two ends comprise normal Watson–Crick pairings but the middle of the helix shows the disymmetric extension and alternate intercalations of unpaired adenines with an interspacing parameter n = 3.3 å. Adenines are shown in blue, guanines in green, cytosines in red and thymines in magenta; the bromine atoms are shown as yellow spheres. Structure 1998 6, 849-861DOI: (10.1016/S0969-2126(98)00087-2)

Figure 2 Comparison of the zipper-like motif to standard B DNA. (a) The zipper-like motif alongside a segment of (b) B DNA. Both structures correspond to an 8 bp stretch (the ninth thymine residue in the zipper-like motif is flipped out of the helix). The zipper-like motif displays the characteristic shape of an X with an elongated phosphodiester backbone. All the adenine bases point in the same direction as the minor groove collapses in the central region. The standard B-DNA structure is more regular and compact. Structure 1998 6, 849-861DOI: (10.1016/S0969-2126(98)00087-2)

Figure 3 Stereo view of the zipper-like motif. A closeup view of the central adenine tract cut out from the duplex. The figure illustrates the substantial buckling of the sheared G·A mismatch located at the bottom of the figure. Atoms are shown in standard colours. Structure 1998 6, 849-861DOI: (10.1016/S0969-2126(98)00087-2)

Figure 4 The cobalt hexammine site. Two views of the cobalt hexammine interactions at the G3 base level, which illustrate the special role of this residue. (a) The 2Fo–Fc map at 2.1 å resolution of the Co(NH3)63+ and the surrounding guanine residues (contoured at 2σ above the mean density with phases from the refined model). (b) Diagram of the extensive hydrogen-bond network linking the Co(NH3)63+ cation around the threefold crystallographic axis to the N7 and O6 atoms of G3. Structure 1998 6, 849-861DOI: (10.1016/S0969-2126(98)00087-2)

Figure 5 Crystal packing. (a) Packing of the structure viewed along the z axis showing the large solvent channel located on the sixfold axes (diameter approximately 18 å). The cobalt hexammine cations lie in narrower channels which also run parallel to the z axis and are located about the threefold axes. (b) Two perpendicular views of the end-to-end packing of duplexes in the crystal structure that generates a continuous helix along the z axis. The asymmetric unit is shown in yellow, its ‘complementary’ strand in red and the stacked symmetry-related helices in green. This duplex is flattened into a ribbon-like structure compared with the standard B DNA double helix. Structure 1998 6, 849-861DOI: (10.1016/S0969-2126(98)00087-2)