ORDERED WATER-STRUCTURE AROUND A BETA-DNA DODECAMER - A QUANTITATIVE STUDY
ORDERED WATER-STRUCTURE AROUND A BETA-DNA DODECAMER - A QUANTITATIVE STUDY
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DOI：
10.1016/0022-2836(83)90033-5
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发表时间：
1983-01-01
影响因子：
5.6
通讯作者：
DICKERSON, RE
中科院分区：
文献类型：
--
作者：
KOPKA, ML;FRATINI, AV;DICKERSON, RE
将序列C-G-C-G-A-A-T-T-C-G-C-G的双螺旋B-DNA十二聚体的晶体结构独立地解析和精制成3种形式：室温下的母体序列; 16 K下的相同序列;和7 ℃下的9-溴变体C-G-C-G-A-A-T-TBrC-G-C-G。C在60%（体积/体积）2-甲基-2，4-戊二醇中的溶液。后2种结构显示出沿磷酸盐主链的广泛水合沿着，这是由于主链原子的高温因素（指示热或静态无序）而在天然结构中不可见的特征。溶剂峰（65）与磷酸盐主链或平均3个/磷酸盐基团相关。十九个其他分子形成的第一壳水化的基础边缘N和O原子内的主要凹槽，和36个以上的发现在上层水化层。后者倾向于以串或簇的形式从一个磷酸基团跨越到另一个磷酸基团。单个精胺分子也横跨大沟。在小沟中，可能主要负责稳定B型DNA的Z字形水合脊柱在所有3种结构中均被发现。小沟的上层水合作用相对稀疏，主要由穿过小沟延伸的水分子串组成，与下面的脊柱接触很少。糖0- 1“原子与水分子密切相关，但这些主要是脊柱中的分子，因此这种关联可能反映了小沟的几何形状，而不是0- 1”原子水合的任何内在吸引力。主链中的磷酸根0- 3“和0- 5”原子是最不水合的，尽管似乎不存在物理或空间障碍来阻止水分子接近这些O原子。
The crystal structure of the double-helical B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G was solved and refined independently in 3 forms: the parent sequence at room temperature; the same sequence at 16 K; and the 9-bromo variant C-G-C-G-A-A-T-TBrC-G-C-G at 7.degree. C in 60% (vol/vol) 2-methyl-2,4-pentanediol. The latter 2 structures show extensive hydration along the phosphate backbone, a feature that was invisible in the native structure because of high temperature factors (indicating thermal or static disorder) of the backbone atoms. Solvent peaks (65) are associated with the phosphate backbone, or an average of 3/phosphate group. Nineteen other molecules form a first shell of hydration to base edge N and O atoms within the major groove, and 36 more are found in upper hydration layers. The latter tend to occur in strings or clusters spanning the major groove from one phosphate group to another. A single spermine molecule also spans the major groove. In the minor groove, the zig-zag spine of hydration that may be principally responsible for stabilizing the B form of DNA is found in all 3 structures. Upper level hydration in the minor groove is relatively sparse, and consists mainly of strings of water molecules extending across the groove, with few contacts to the spine below. Sugar 0-1'' atoms are closely associated with water molecules, but these are chiefly molecules in the spine, so the association may reflect the geometry of the minor groove rather than any intrinsic attraction of 0-1'' atoms for hydration. The phosphate 0-3'' and 0-5'' atoms within the backbone chain are least hydrated of all, although no physical or steric impediment seems to exist that would deny access to these O atoms by water molecules.