J Am Chem Soc. 2020 Mar 18;142(11):5204-5211. doi: 10.1021/jacs.9b12770. Epub 2020 Mar 9.
Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.
PDGFR-β 的异常表达与许多疾病有关。PDGFR-β 基因启动子中形成的 G-四链体（G4s）是转录调节剂，可靶向小分子。先前已显示 PDGFR-β 基因启动子中形成的主要 G4 具有断裂的 G-链。在此，我们报告 PDGFR-β 基因启动子序列形成空位 G-四链体（vG4），可被生理相关的鸟嘌呤代谢物（如 dGMP、GMP 和 cGMP）以及鸟嘌呤衍生物药物填充和稳定。我们确定了 K 溶液中 dGMP 填充的 PDGFR-β vG4 的 NMR 结构。这是第一个基于人类基因启动子序列的鸟嘌呤代谢物填充 vG4 的结构。我们的结构和系统分析阐明了 Hoogsten 氢键、糖和磷酸部分对特定 G-空位填充的贡献。有趣的是，PDGFR-β 启动子序列中存在 3'-和 5'-末端 vG4 的平衡，并且 dGMP 有利于 5'-末端填充。测试了鸟嘌呤代谢物和药物，它们对 5'-空位表现出保守的选择性，除了 cGMP。cGMP 结合 3'-和 5'-末端 vG4 并形成具有相似群体的两个填充 G4。重要的是，鸟嘌呤代谢物参与人类细胞中的许多生理和病理过程；因此，我们的结果为通过与启动子 vG4 相互作用了解它们的潜在调节功能提供了结构基础。此外，NMR 结构可以指导针对 PDGFR-β vG4 的配体的合理设计。
