Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA.
Nucleic Acids Res. 2021 May 7;49(8):4782-4792. doi: 10.1093/nar/gkab264.
Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.
即使在分辨率为 1Å 或更高的高质量 X 射线寡核苷酸晶体结构中，第一壳层水分子的取向仍然不清楚。我们使用冷冻中子晶体学来深入了解左手 Z-DNA 双链体 [d(CGCGCG)]2 周围水分子的氢键模式。首次在 1.5Å 分辨率下可视化的中子密度使我们能够直接确定与 DNA直接接触的大多数水分子和许多第二壳层水分子的取向。特别是，水参与小沟内突出的水合模体、凸面或桥连碱基和磷酸氧原子的氢键供体和受体模式最终被揭示。一些水分子显示出完全出乎意料的取向。例如，位于氢键距离内的水分子两个相邻鸟嘌呤的 O6 酮氧原子直接将其两个氘原子远离酮基团。鸟嘌呤（N2）和胞嘧啶（N4）的环外氨基出人意料地稳定了与相邻胞嘧啶的 O2 酮氧原子和与相邻鸟嘌呤的 O6 酮氧原子氢键结合的水。我们的结构提供了迄今为止最详细的固态 DNA 溶剂化视图，不受金属离子或聚胺的影响。
