Kennard O, Cruse W B, Nachman J, Prange T, Shakked Z, Rabinovich D
University Chemical Laboratory, Cambridge, England.
J Biomol Struct Dyn. 1986 Feb;3(4):623-47. doi: 10.1080/07391102.1986.10508452.
The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.
使用衍射仪和同步加速器数据相结合的方法，将脱氧八聚体d(G-G-BrU-A-BrU-A-C-C)的晶体结构精修至1.7 Å的分辨率。在两个实验室中分别采用不同的程序独立进行分析。尽管最终结果相同，但两种方法的比较突出了在仅有有限数据时寡核苷酸精修中存在的潜在问题。作为分析的一部分，确定了不对称单元中84个溶剂分子的位置。DNA分子高度水合，尤其是磷酸 - 糖主链和碱基的官能团。在中央BrU-A-BrU-A区域的大沟中，有一条水分子带，形成共享边的封闭五边形。这些水分子与碱基的O和N原子以及连接每条链上O-1磷酸氧原子的溶剂链相连。小沟也被广泛水合，在中央区域有一个连续的网络，两端各有其他网络。简要比较了这种水合模式与在B - 十二聚体结构中观察到的模式。
