The High Resolution Structure of DNA by Single-Crystal X-Ray Methods

The crystal structures of two synthetic DNA oligomers have been solved and refined. The first, a tetramer of base sequence d(CpGpCpG) or CGCG, crystallizes as four-base-pair fragment of left-handed Z' double helix. It differs from the Z helix adopted by the related hexamer sequence CGCGCG in that the pucker of guanine sugar rings is C1'-exo rather than C3'-endo. Crystals of the tetramer, grown from an exceptionally high-salt solution, incorporate excess magnesium chloride. The magnesium cations do not appear to play any structural role, but chloride anions, bound to guanine 2-amino groups in the minor groove, may induce the C3'-endo/C1-exo guanine sugar pucker change via electrostatic repulsion of a nearby phosphate oxygen. A second compound, the dodecamer CGCGAATTCGCG, crystallizes as slightly more than a full turn of right-handed B-DNA. The fact that both CGCG ends of this molecule remain right-handed, without a trace of any conformational instability, implies that left-right interfaces and left-handed helical regions might be rare or nonexistent in a DNA polymer of mixed sequence. Although the dodecamer double helix is smoothly deformed into a radius of curvature of 110 Å, bending has little effect on local helix parameters. Instead, the sequence of bases along the chain plays a more important role in helix variability. Purine sugars exhibit the C2'-endo pucker of classical B-DNA, but pyrimidine sugars are distorted into a conformation intermediate between 01'-endo and C1'-exo. Because sugar pucker and glycosyl angle are closely related parameters, this small difference in sugar pucker leads to subtle sequence-specific variations in base pair position and helix twist. In general, pyrimidine-purine steps open to the minor groove, while purine-pyrimidine steps open to the major. Ordered water molecules are an integral part of the CGCGAATTCGCG structure, and they are found more in the grooves of the helix than in the first coordination shell of phosphate groups. Major groove waters are predominantly monodentate, but those in the GAATTC minor groove are organized into a single cooperative network or "spine" that extends from the surface of the base pairs to beyond the helical radius of phosphate oxygens. The inner two shells of this network exhibit hydrogen-bonded geometries which are likely to be specific for an uninterrupted stretch of A/T base pairs.