Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
Academy of Scientific and Innovative Research, Ghaziabad 201002, India.
ACS Appl Bio Mater. 2024 Nov 18;7(11):7233-7243. doi: 10.1021/acsabm.4c00940. Epub 2024 Oct 28.
Guanine-rich DNA/RNA sequences can form Hoogsteen bonds to adopt noncanonical secondary structures called G-quadruplexes, and these have been associated with diverse cellular processes. There has been considerable research interest in the design of G4-interacting ligands for cellular probing of the G4 structure and understanding its associated biological function. Most of the fluorescent G4 ligands either do not have significant selectivity over other nucleic acid structures, have high Stokes shift, or are not in the near-infrared (NIR) region, which limits its cellular visualization. The current work involves the rational design and synthesis of NIR fluorescent probes comprising a (Z)-1-methyl-2-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium scaffold. Among the designed molecules, exhibited far-red fluorescence (λ = 680 nm) with large Stokes shift (∼182 nm) upon selective binding to human telomeric G-quadruplexes. The dye does not disturb the conformation and stability of G-quadruplexes, thereby making it suitable for nucleic acid research based applications. Interestingly, showed remarkable selectivity over single- and double-stranded structures in contrast to a commercially available quadruplex binding probe, Thiazole orange (TO). The molecular docking studies indicate that binds at the groove region of the telomeric DNA G-quadruplex through π-π stacking interactions with the quinoline and amine-substituted phenyl ring and with the phosphate backbone through anion-π interactions with the benzothiazole ring. The designed molecule has interesting photophysical properties, cell permeability, and biocompatibility with minimal cytotoxicity. Fluorescence imaging studies in live HeLa cells showed that probe binds to the transient population of the DNA G-quadruplex in the nucleus and RNA quadruplexes in the cytoplasm. In brief, G-quadruplex NIR fluorescent probe with a higher signal/noise ratio has significant potential for cellular imaging studies and thus opens avenues to decipher the biological pathways for better understanding of G-quadruplex biology.
富含鸟嘌呤的 DNA/RNA 序列可以形成 Hoogsteen 键，从而形成称为 G-四链体的非经典二级结构，这些结构与多种细胞过程有关。人们对设计与 G4 相互作用的配体产生了相当大的研究兴趣，这些配体可用于细胞探测 G4 结构并了解其相关的生物学功能。大多数荧光 G4 配体要么对其他核酸结构没有显著选择性，要么 Stokes 位移较大，要么不在近红外 (NIR) 区域，这限制了其在细胞中的可视化。目前的工作涉及包含 (Z)-1-甲基-2-((3-甲基苯并[d]噻唑-2(3H)-亚基)甲基)喹啉-1-翁支架的 NIR 荧光探针的合理设计和合成。在所设计的分子中， 表现出远红色荧光（λ = 680nm），具有较大的 Stokes 位移（∼182nm），选择性结合于人端粒 G-四链体。该染料 不会干扰 G-四链体的构象和稳定性，因此使其适用于基于核酸的研究应用。有趣的是， 与市售的四链体结合探针噻唑橙 (TO) 相比，对单链和双链结构具有显著的选择性。分子对接研究表明， 通过与喹啉和胺取代的苯基环的 π-π 堆积相互作用以及与苯并噻唑环的阴离子-π 相互作用， 在端粒 DNA G-四链体的沟槽区域与四链体结合。设计的分子 具有有趣的光物理性质、细胞通透性和生物相容性，细胞毒性最小。在活 HeLa 细胞中的荧光成像研究表明，探针 与细胞核中 DNA G-四链体的瞬态群体以及细胞质中的 RNA 四链体结合。简而言之，具有更高信噪比的 G-四链体近红外荧光探针 具有用于细胞成像研究的巨大潜力，因此为阐明生物学途径开辟了道路，从而更好地理解 G-四链体生物学。
