Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany.
Angew Chem Int Ed Engl. 2021 Feb 23;60(9):4939-4947. doi: 10.1002/anie.202008618. Epub 2020 Nov 30.
DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine) complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu -Cu distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates.
DNA G-四链体表现出形成高阶结构的明显趋势，例如π堆积二聚体和与芳香族结合伴侣的聚集体。可靠的方法来确定这些非共价加合物的结构是稀缺的。在这里，我们使用人工正方形平面 Cu（吡啶）配合物，共价结合到四聚体 G-四链体中，作为刚性自旋标记物，通过脉冲偶极子 EPR 光谱检测二聚体结构和测量分子间 Cu-Cu 距离。一系列不同空间尺寸的 G-四链体二聚体，以尾对尾或头对头堆叠模式形成，可明确区分。测量的距离与分子动力学模拟的结果完全一致。此外，还研究了两种众所周知的 G-四链体结合物 PIPER 和端粒酶抑制剂掺入导致夹心复合物的 G-四链体二聚体，发现了以前未知的结合模式。此外，我们还提供了自由 G-四联体也插入二聚体的证据。我们的过渡金属标记方法与脉冲 EPR 光谱相结合，为研究非共价 DNA 聚集体的结构开辟了新的可能性。
