Jean Y C, Gao Y G, Wang A H
Biophysics Division, University of Illinois at Urbana-Champaign 61801.
Biochemistry. 1993 Jan 12;32(1):381-8. doi: 10.1021/bi00052a047.
Oligonucleotides with modification at the 5'-end have been used for various biochemical applications. As a first step to better assess the effects of those modifications on DNA conformation, we determined at 1.4-A resolution the left-handed Z-DNA structure of a DNA hexamer, aminohexyl-5'-d(pCpGp[br5C]pGpCpG), by X-ray diffraction analysis. This hexamer was crystallized in the monoclinic C2 (a = 51.13 A, b = 18.44 A, c = 34.67 A, and beta = 120.9 degrees) space group. Its structure has been refined by the restrained least-squares refinement to a final R factor of 0.164 using 3727 [> 2.0 sigma (F)] observed reflections. The overall conformation of the double helix resembles that of the canonical Z-DNA. The terminal 5'-phosphate groups of the dC residues adopt conformations (beta approximately 180 degrees and gamma approximately 60 degrees) similar to phosphodiester's conformation of the internal dC residues. Two types of interhelical stackings are observed, one of which may serve as a model for a single-strand nick in the backbone of DNA double helix. A barium ion is found to bridge two side-by-side Z-DNA helices by coordinating to the O6 and N7 atoms of two guanines simultaneously. This "cross-linking" ability of barium ion may be a useful property in promoting the reversible aggregation of nucleic acids.
5'-端有修饰的寡核苷酸已用于各种生化应用。作为更好地评估这些修饰对DNA构象影响的第一步，我们通过X射线衍射分析，以1.4埃的分辨率确定了一个DNA六聚体（氨基己基-5'-d(pCpGp[br5C]pGpCpG)）的左手Z-DNA结构。该六聚体在单斜C2（a = 51.13埃，b = 18.44埃，c = 34.67埃，β = 120.9°）空间群中结晶。其结构已通过约束最小二乘精修，使用3727个[> 2.0σ(F)]观测反射，精修至最终R因子为0.164。双螺旋的整体构象类似于典型的Z-DNA。dC残基的末端5'-磷酸基团采取的构象（β约180°，γ约60°）类似于内部dC残基的磷酸二酯构象。观察到两种类型的螺旋间堆积，其中一种可作为DNA双螺旋主链中单链切口的模型。发现一个钡离子通过同时与两个鸟嘌呤的O6和N7原子配位，桥接两个并排的Z-DNA螺旋。钡离子的这种“交联”能力可能是促进核酸可逆聚集的一种有用特性。
