Dong Xiangchao
Department of Chemistry, Hunter College of The City University of New York, New York, NY 10071, USA.
Acta Crystallogr D Biol Crystallogr. 2003 Jul;59(Pt 7):1336-8. doi: 10.1107/s0907444903009211. Epub 2003 Jun 27.
Determination of the binding positions of light metal ions in the structure of oligonucleotides remains a challenge owing to their irregular coordination geometries, low electron densities and mobility in the crystals. To study the interactions between monovalent cations and DNA, the heavier alkali metal ion Rb(+) was used to replace Na(+) and K(+) in the Z-DNA crystal and the structure was analyzed using X-ray cryocrystallography. The resolution of the Rb-d(CGCGCG)(2) crystal data set is 1.76 A, with an R(merge) of 0.061. The final residual factor (R factor) for the crystal structure is 0.175. The positions of 16 Rb(+) ions were tentatively assigned, with most of them having partial occupancies. Three rubidium ions with full occupancies coordinated to two DNA double strands were located in the Z-DNA crystal. The results of this work suggest that there are numerous relatively low-energy sites for binding of monovalent cations to Z-DNA and that these sites are cation-water hybrid positions.
由于轻金属离子在寡核苷酸结构中的配位几何形状不规则、电子密度低且在晶体中具有流动性，确定其结合位置仍然是一项挑战。为了研究单价阳离子与DNA之间的相互作用，在Z-DNA晶体中使用较重的碱金属离子Rb(+)替代Na(+)和K(+)，并使用X射线低温晶体学分析其结构。Rb-d(CGCGCG)(2)晶体数据集的分辨率为1.76 Å，合并R因子（R(merge)）为0.061。晶体结构的最终残余因子（R因子）为0.175。初步确定了16个Rb(+)离子的位置，其中大多数具有部分占有率。在Z-DNA晶体中发现了三个占有率为100%的铷离子与两条DNA双链配位。这项工作的结果表明，单价阳离子与Z-DNA结合存在许多能量相对较低的位点，这些位点是阳离子-水混合位置。
