Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States.
Department of Pharmacy, Daping Hospital, Army Medical University, Chongqing 400042, China.
Biochemistry. 2020 Sep 22;59(37):3438-3446. doi: 10.1021/acs.biochem.0c00351. Epub 2020 Sep 3.
Although allosteric binding of small molecules is commonplace in protein structures, it is rather rare in DNA species such as G-quadruplexes. By using CD melting, here, we found binding of the small-molecule ligands PDS and L2H2-6OTD to the telomeric DNA G-quadruplex was cooperative. Mass spectrometry indicated a 1:1:1 ratio in the ternary binding complex of the telomeric G-quadruplex, PDS, and L2H2-6OTD. Compared to the binding of each individual ligand to the G-quadruplex, single-molecule mechanical unfolding assays revealed a significantly decreased dissociation constant when one ligand is evaluated in the presence of another. This demonstrates that cooperative binding of PDS and L2H2-6OTD to the G-quadruplex is allosteric, which is also supported by the mass spectra data that indicated the ejection of coordinated sodium ions upon binding of the heteroligands to the G-quadruplex. The unprecedented observation of the allosteric ligand binding to higher-ordered structures of DNA may help to design more effective ligands to target non-B DNA species involved in many critical cellular processes.
尽管小分子的变构结合在蛋白质结构中很常见，但在 DNA 物种如 G-四链体中却相当罕见。通过使用 CD 熔融，我们发现小分子配体 PDS 和 L2H2-6OTD 与端粒 DNA G-四链体的结合具有协同性。质谱分析表明，在端粒 G-四链体、PDS 和 L2H2-6OTD 的三元结合复合物中，存在 1:1:1 的比例。与每个单独配体与 G-四链体的结合相比，单分子机械解折叠测定显示，当一个配体在另一个配体存在的情况下进行评估时，解离常数显著降低。这表明 PDS 和 L2H2-6OTD 与 G-四链体的协同结合是变构的，这也得到了质谱数据的支持，表明在异配体与 G-四链体结合时，配位钠离子被排出。这种对 DNA 高级结构的变构配体结合的前所未有的观察结果，可能有助于设计更有效的配体，以靶向涉及许多关键细胞过程的非 B DNA 物种。
