title: Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations.
abstract: The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2'-deoxyribose (the natural enantiomer) and L-2'-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg2+sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA-Mg2+structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG)2duplex with those of other homochiral and heterochiral Z-DNA structures.
authors.affiliation: Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
authors.forename: Pawel
authors.initials: P
authors.lastname: Drozdzal
authors.affiliation: Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
authors.forename: Miroslaw
authors.initials: M
authors.lastname: Gilski
authors.affiliation: Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Jaskolski
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D018360:Crystallography, X-Ray; D043542:DNA, Z-Form / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013237:Stereoisomerism
chemical_list: D043542:DNA, Z-Form; D009841:Oligonucleotides
keywords: Z-DNA; centrosymmetric space group; dual-conformation backbone; dual-conformation base pairs; dual-conformation nucleic acid; intermolecular base stacking; racemate