Structure of a B-DNA Dodecamer: Conformation and Dynamics
The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-angstrom resolution (two-sigma data). The molecule forms slightly more than one complete turn of righthanded double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 21 screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A·T base pairs in the center of the molecule is 17.3 degrees, and that between C· G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta , exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg=123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta . A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired bases appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta =123 degrees. This same anticorrelation is also observed in other DNA and DNA· RNA structures.