Z-DNA Structure of a Modified DNA Hexamer at 1.4-Å Resolution: Aminohexyl- 5′-d(pCpGp [br⁵C] pGpCpG

Oligonucleotides with modification at the 5′-end have been used for various biochemical applications. As a first step to better assess the effects of those modifications on DNA conformation, we determined at 1.4-Å resolution the left-handed Z-DNA structure of a DNA hexamer, aminohexyl-5′- d(pCpGp[br⁵C]pGpCpG), by X-ray diffraction analysis. This hexamer was crystallized in the monoclinic C2 (a = 51.13 Å, b = 18.44 Å, c = 34.67 Å, and β = 120.9°) space group. Its structure has been refined by the restrained least-squares refinement to a final R factor of 0.164 using 3727 [>2.0σ(F)] observed reflections. The overall conformation of the double helix resembles that of the canonical Z-DNA. The terminal 5′-phosphate groups of the dC residues adopt conformations (β ∼180° and γ ∼ 60°) similar to phosphodiester's conformation of the internal dC residues. Two types of interhelical stackings are observed, one of which may serve as a model for a single-strand nick in the backbone of DNA double helix. A barium ion is found to bridge two side-by-side Z-DNA helices by coordinating to the O6 and N7 atoms of two guanines simultaneously. This “cross-linking” ability of barium ion may be a useful property in promoting the reversible aggregation of nucleic acids.