More is not always better: finding the right trade-off between affinity and selectivity of a G-quadruplex ligand
作者:Michela Zuffo、Aurore Guédin、Emma-Dune Leriche、Filippo Doria、Valentina Pirota、Valérie Gabelica、Jean-Louis Mergny、Mauro Freccero
DOI:10.1093/nar/gky607
日期:2018.11.2
Guanine-rich nucleic acid sequences can fold into four-stranded G-quadruplex (G4) structures. Despite growing evidence for their biological significance, considerable work still needs to be done to detail their cellular occurrence and functions. Herein, we describe an optimized core-extended naphthalene diimide (cex-NDI) to be exploited as a G4 light-up sensor. The sensing mechanism relies on the shift of the aggregate-monomer equilibrium towards the bright monomeric state upon G4 binding. In contrast with the majority of other ligands, this novel cex-NDI is able to discriminate among G4s with different topologies, with a remarkable fluorescent response for the parallel ones. We investigate this sensing by means of biophysical methods, comparing the lead compound to a non-selective analogue. We demonstrate that mitigating the affinity of the binding core for G4s results in an increased selectivity and sensitivity of the fluorescent response. This is achieved by replacing positively charged substituents with diethylene glycol (DEG) side chains. Remarkably, the limit of detection values obtained for parallel G4s are more than one order of magnitude lower than those of the parallel-selective ligand N-methyl mesoporphyrin IX (NMM). Interestingly, the classical fluorescent intercalator displacement (FID) assay failed to reveal binding of cex-NDI to G4 because of the presence a ternary complex (G4-TO-cex-NDI) revealed by electrospray-MS. Our study thus provides a rational basis to design or modify existent scaffolds to redirect the binding preference of G4 ligands.
富含鸟嘌呤的核酸序列可以折叠成四链 G-四重态(G4)结构。尽管越来越多的证据表明它们在生物学上的重要性,但仍需进行大量工作以详细了解它们在细胞中的出现和功能。在此,我们描述了一种优化的核心扩展萘二酰亚胺(cex-NDI),可用作 G4 亮灯传感器。该传感机制依赖于 G4 结合时聚集-单体平衡向明亮单体状态的转移。与大多数其他配体相比,这种新型的 cex-NDI 能够辨别不同拓扑结构的 G4,并对平行结构表现出显著的荧光响应。我们通过生物物理方法研究这种传感,将领先化合物与非选择性类似物进行比较。我们证明,减弱结合核心对 G4 的亲和力会提高荧光响应的选择性和灵敏度。此项改进是通过用二乙二醇(DEG)侧链替换带正电的取代基实现的。值得注意的是,平行 G4 的检测限值比平行选择性配体 N-甲基介孔卟啉 IX(NMM)的检测限值低一个数量级以上。有趣的是,经典的荧光插层位移(FID)测定未能揭示 cex-NDI 与 G4 的结合,因为通过电喷雾质谱(MS)显示了三元复合物(G4-TO-cex-NDI)的存在。因此,我们的研究为设计或修改现有骨架以重新引导 G4 配体的结合偏好提供了合理基础。