D. Bancroft et al., THE LOW-TEMPERATURE CRYSTAL-STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR-GROOVE, Biochemistry, 33(5), 1994, pp. 1073-1086
The X-ray crystal structure of the pure-spermine form of the left-hand
ed Z-DNA duplex [d(CGCGCG)](2) has been determined at a temperature of
-110 degrees C. Whereas the previously described room temperature str
ucture of the pure-spermine form showed only the presence of a single
''interhelix'' spermine molecule, mediating contacts between neighbori
ng duplexes (Egli et al., 1991), a second ''intrahelix'' spermine mole
cule as well as two hydrated sodium ions were found in the structure d
etermined at low temperature. This second spermine molecule binds prim
arily within the minor groove of two hexamer duplexes that are stacked
in an end-to-end fashion in the crystal lattice. Thus, the intrahelix
spermine molecule interacts with a single infinite helix. The spine o
f hydration observed in other structures of Z-DNA hexamers is partiall
y replaced and partially displaced by the intrahelix spermine molecule
. In Z-DNA, phosphate groups are relatively closely spaced across the
minor groove compared to the right-handed double-helical conformation
of B-DNA. The intrahelix spermine molecule decreases cross-groove elec
trostatic repulsion within the Z-DNA helix, thereby increasing its rel
ative stability. This structure may therefore provide an explanation f
or the role of spermine as a very effective inducer of the conformatio
nal B-DNA to Z-DNA transition with alternating dG-dC sequences in solu
tion.