Department of Electronic Science and Engineering, Kyoto University, Kyoto University Katsura, Nishikyo, Kyoto, 615-8510, Japan.
Sci Rep. 2019 May 2;9(1):6851. doi: 10.1038/s41598-019-42394-5.
The DNA in the left-handed conformation (Z-conformation) was first discovered by A. Rich, who revealed the crystalline structure of a DNA oligomer d(GC) by X-ray diffraction method. Later it was also found that DNA molecules change their conformations from typical right-handed form (B-DNA) to the left-handed form (Z-DNA) under specific conditions (B-Z transition). Furthermore, the detailed structures of the interface between B- and Z-DNAs, B-Z junction, was also determined with an atomic resolution. Recently it was found that some proteins have the Z-DNA binding domains, but the biological functions of Z-DNA are not well understood yet. Therefore the investigation of Z-DNA under physiological conditions is highly essential. In this study, we demonstrated the high-resolution real-space imaging of DNA molecules having the Z- and B-form conformations by frequency-modulation atomic force microscopy (FM-AFM), that has made a great progress in recent years, in an aqueous solution. The major and minor grooves of both DNA conformations were clearly visualized. Furthermore, the surface charge density was measured by three-dimensional (3D) force mapping method. We found that Z-form region was less negatively charged than the B-form region.
左手构象（Z 构象）中的 DNA 最初是由 A. Rich 发现的，他通过 X 射线衍射法揭示了 DNA 寡聚物 d(GC)的晶体结构。后来还发现，在特定条件下（B-Z 转换），DNA 分子会从典型的右手构象（B-DNA）转变为左手构象（Z-DNA）。此外，B-DNA 和 Z-DNA 之间的界面，即 B-Z 接头的详细结构也以原子分辨率确定。最近发现，一些蛋白质具有 Z-DNA 结合结构域，但 Z-DNA 的生物学功能尚未得到很好的理解。因此，在生理条件下研究 Z-DNA 非常重要。在这项研究中，我们通过近年来取得重大进展的调频原子力显微镜（FM-AFM）在水溶液中对具有 Z 构象和 B 构象的 DNA 分子进行了高分辨率实时成像。两种构象的主沟和小沟都清晰可见。此外，我们还通过三维（3D）力映射法测量了表面电荷密度。我们发现 Z 构象区域的负电荷密度低于 B 构象区域。
