Open AccessPhosphates in the Z‐DNA dodecamer are flexible, but their P‐SAD signal is sufficient for structure solution
Author(s) -
Luo Zhipu,
Dauter Miroslawa,
Dauter Zbigniew
Publication year - 2014
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s1399004714004684
Subject(s) - dodecameric protein , random hexamer , crystallography , duplex (building) , dna , crystal structure , molecule , chemistry , stacking , helix (gastropod) , resolution (logic) , molecular physics , biology , ecology , biochemistry , organic chemistry , snail , artificial intelligence , computer science
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.