Z-DNA STRUCTURE OF A MODIFIED DNA HEXAMER AT 1.4-A 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-angstrom 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 angstrom, b = 18.44 angstrom, c = 34.67 angstrom, and beta = 120.9-degrees) space group. Its structure has been refined by the restrained least-squares refinement to a final R factor of 0.164 using 3727 [>2.0sigma(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 (beta approximately 180-degrees and gamma approximately 60-degrees) 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.