title: Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution.
abstract: A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix.
authors.affiliation: Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Zhipu
authors.initials: Z
authors.lastname: Luo
authors.affiliation: Leidos Biomedical Research Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Miroslawa
authors.initials: M
authors.lastname: Dauter
authors.affiliation: Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Zbigniew
authors.initials: Z
authors.lastname: Dauter
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D018360:Crystallography, X-Ray; D043542:DNA, Z-Form / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry*
chemical_list: D001704:Biopolymers; D043542:DNA, Z-Form; D010710:Phosphates
keywords: Z-DNA dodecamer; Z-DNA structure; flexibility of phosphate groups; phosphorus SAD phasing; ultrahigh resolution