Atomic resolution structure of a chimeric DNA–RNA Z-type duplex in complex with Ba2+ions: a case of complicated multi-domain twinning

Abstract

The self-complementary dCrGdCrGdCrG hexanucleotide, in which not only the pyrimidine/purine bases but also the ribo/deoxy sugars alternate along the sequence, was crystallized in the presence of barium cations in the form of a left-handed Z-type duplex. The asymmetric unit of theP21crystal with a pseudohexagonal lattice contains four chimeric duplexes and 16 partial Ba2+sites. The chimeric (DNA–RNA)2duplexes have novel patterns of hydration and exhibit a high degree of discrete conformational disorder of their sugar-phosphate backbones, which can at least partly be correlated with the fractional occupancies of the barium ions. The crystals of the DNA–RNA chimeric duplex in complex with Ba2+ions and also with Sr2+ions exhibit complicated twinning, which in combination with structural pseudosymmetry made structure determination difficult. The structure could be successfully solved by molecular replacement in space groupsP1 andP21but not in orthorhombic or higher symmetry and, after scrupulous twinning and packing analysis, was refined in space groupP21to anRandRfreeof 11.36 and 16.91%, respectively, using data extending to 1.09 Å resolution. With the crystal structure having monoclinic symmetry, the sixfold crystal twinning is a combination of threefold and twofold rotations. The paper describes the practical aspects of dealing with cases of complicated twinning and pseudosymmetry, and compares the available software tools for the refinement and analysis of such cases.