UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
National Center for CryoEM Access and Training (NCCAT), Simons Electron Microscopy Center, New York Structural Biology Center, NY 10027, USA.
Nucleic Acids Res. 2023 Feb 28;51(4):1943-1959. doi: 10.1093/nar/gkad014.
Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5' G-tetrad interface with a persistently unstacked 3' duplex. The surrogate complement poly dT loop preferably stacks onto the 3' G-tetrad interface resulting in occlusion of both 5' and 3' tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.
富含鸟嘌呤的基因组区域可以折叠成非 B 型 DNA 四链结构，称为 G-四链体 (G4s)。广泛的体内研究表明，启动子 G4 是转录调节剂。对于这些嵌入双链体中的 G4 结构，即它们假定的基因组环境，几乎没有结构信息。在这里，我们使用 cryo-EM、分子动力学和小角 X 射线散射 (SAXS) 研究报告了一个 28.5 kDa 双链体-G4-双链体 (DGD) 模型系统的 7.4 Å 分辨率结构和动力学。DGD cryo-EM 精制模型的特点是在 5' G-四联体界面处由堆叠的双链体-G4 相互作用诱导的 53°弯曲，3' 双链体保持未堆叠。替代互补多 dT 环优选堆积在 3' G-四联体界面上，导致 5' 和 3' 四联体界面都被封闭。结构分析表明，DGD 模型比单体 G4 结构更具可药性，代表了一个新的结构药物靶标。我们的结果说明了 cryo-EM、MD 和 SAXS 的集成如何能够揭示 DNA G4 系统的互补详细静态和动态结构信息。
