Crystal structure of a Z-DNA hexamer d(CGCICG) at 1.7 ? resolution: inosine-cytidine base-pairing, and comparison with other Z-DNA structures

摘要

The crystal structure of the deoxyhexamer, d(CGCICG), has been determined and refined to a resolution of 1.7?. The DNA hexamer crystallises in space group P212121 with unit cell dimensions of a = 18.412 ≠ .017 A, b = 30.485≠.036A, and c = 43.318≠.024 A. The structure has been solved by rotation and translation searches and refined to an R-factor of 0.148 using 2678 unique reflections greater than 1.0 σ (F) between 10.0-1.7 ? resolution. Although the crystal parameters are similar to several previously reported Z-DNA hexamers, this Inoslne containing Z-DNA differs in the relative orientation, position, andcrystal packing Interactions compared to d(CGCGCG) DNA. Many of these differences in the inoslne form of Z-DNA can be explained by crystal packing Interactions, which are responsible for distortions of the duplex at different locations. The most noteworthy features of the inoslne form of Z-DNA as a result of such distortions are: (1) sugar puckers for the inoslnes are of C4'-exo type, (2) all phosphates have the Z1 conformation, and (3) narrower minor grove and compression along the helical axis compared to d(CGCGCG) DNA. In addition, the substitution of guanoslne by Inosine appears to have resulted in Watson-Crick type base-pairing between Inoslne and cytidine with a potential bifurcated hydrogen bond between Inoslne N1 and cytidine N3 (2.9 ?) and 02 (3.3-3.?).