Structure of the Pure - Spermine Form of Z - DNA ( Magnesium Free ) at 1 - 8 , Resolution + , *

We describe the three-dimensional X-ray structure of a complex of spermine bound to a Z-DNA duplex, [d(CGCGCG)],, in the absence of any inorganic polyvalent cations. We have crystallized the D N A hexamer d(CGCGCG) in the exclusion of magnesium and other polyvalent ions and solved its structure a t 1 .O-A resolution. In the crystal of this pure-spermine form of Z-DNA, the relative orientation, position, and interactions of the D N A differ from the arrangement uniformly observed in over a dozen previously reported Z-DNA hexamers. Moreover, the conformation of the Z-DNA hexamer in this structure varies somewhat from those found in earlier structures. The DNA is compressed along the helical axis, the base pairs are shifted into the major groove, and the minor groove is more narrow. The packing of spermineDNA complexes in crystals suggests that the molecular basis for the tendency of spermine to stabilize compact D N A structures derives from the capacity of spermine to interact simultaneously with several duplexes. This capacity is maximized by both the polymorphic nature and the length of the spermine cation. The length and flexibility of spermine and the dispersion of charge-charge, hydrogen-bonding, and hydrophobic bonding potential throughout the molecule maximize the ability of spermine to interact simultaneously with different D N A molecules. Condensa t ion of DNA into compact structures is cation and McCann (1982), Tabor and Tabor (1984), and Feuerstein dependent. The focus of this report is spermine, a member et al. (1991)l. Spermine is the largest polyamine found in of a complex and nearly ubiquitous family of biological cations eukaryotes and, with a positive charge of 4 at pH 7, also the known as the polyamines [for reviews, see Morris (1981), Pegg most highly charged. A series of larger polyamines (pentamines and hexamines) have been isolated from thermophilic This research was supported by grants from the National Institutes bacteria. Spermine stabilizes duplex DNA against thermal of Health, the American Cancer Society, the National Science Foundadenaturation (Mandel, 1962; Tabor, 1962; Bloomfield & tion, the Office of Naval Research, and the National Aeronautics and wilson, 1 9 8 ~ ; Thomas & ~ l ~ ~ f i ~ l d , 1984) and can condense Space Administration. M.E. acknowledges fellowship support by the Geigy-Jubilaums-Stiftung. L.D.W. acknowledges fellowship support by DNA Schellman$ 978; Chattoraj et al.$ 978; the National Institutes of Health and the Medical Foundation, Boston, Wilson & Bloomfield, 1979; Widom 8~ Baldwin, 1980) and MA. chromatin (Sen & Crothers, 1986) into compact structures. * To whom correspondence should be addressed. We describe the three-dimensional X-ray structure of a complex of spermine bound to a Z-DNA duplex. Z-DNA was *The atomic coordinates have been deposited with the Brookhaven f Current address: Analytical Research Department, Bristol Myersfirst detected with CD spectroscopy (Pohl & J o v h 197% and the three-dimensional structure of the Z conformation of [dProtein Data Bank (entry number 1D48). Squibb, Wallingford, CT 06492. 0006-2960/91/0430-11388%02.50/0