Abrahamsson Alva, Berner Andreas, Golebiewska-Pikula Justyna, Chaudhari Namrata, Keskitalo Emelie, Lindgren Cecilia, Chmielewski Marcin K, Wanrooij Sjoerd, Chorell Erik
Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.
Departments of Medical Biochemistry and Biophysics, Umea University, SE-907 36 Umeå, Sweden.
Bioconjug Chem. 2025 Apr 16;36(4):724-736. doi: 10.1021/acs.bioconjchem.5c00008. Epub 2025 Mar 20.
G-quadruplex (G4) DNA structures are noncanonical secondary structures found in key regulatory regions of the genome, including oncogenic promoters and telomeres. Small molecules, known as G4 ligands, capable of stabilizing G4s hold promise as chemical probes and therapeutic agents. Nevertheless, achieving precise specificity for individual G4 structures within the human genome remains a significant challenge. To address this, we expand upon G4-ligand-conjugated oligonucleotides (GL-Os), a modular platform combining the stabilizing properties of G4-ligands with the sequence specificity of guide DNA oligonucleotides. Central to this strategy is the linker that bridges the G4 ligand and the guide oligonucleotide. In this study, we develop multiple conjugation strategies for the GL-Os that enabled a systematic investigation of the linker in both chemical composition and length, enabling a thorough assessment of their impact on targeting oncogenic G4 DNA. Biophysical, biochemical, and computational evaluations revealed GL-Os with optimized linkers that exhibited enhanced binding to target G4s, even under thermal or structural stress. Notably, longer linkers broadened the range of targetable sequences without introducing steric hindrance, thereby enhancing the platform's applicability across diverse genomic contexts. These findings establish GL-Os as a robust and versatile tool for the selective targeting of individual G4s. By facilitating precise investigations of G4 biology, this work provides a foundation for advancing G4-targeted therapeutic strategies and exploring their role in disease contexts.
G-四链体（G4）DNA结构是在基因组关键调控区域发现的非规范二级结构，包括致癌启动子和端粒。能够稳定G4的小分子，即G4配体，有望成为化学探针和治疗剂。然而，实现对人类基因组中单个G4结构的精确特异性识别仍然是一项重大挑战。为了解决这个问题，我们扩展了G4配体共轭寡核苷酸（GL-Os），这是一个模块化平台，它将G4配体的稳定特性与引导DNA寡核苷酸的序列特异性结合起来。该策略的核心是连接G4配体和引导寡核苷酸的接头。在这项研究中，我们为GL-Os开发了多种共轭策略，能够系统地研究接头的化学成分和长度，从而全面评估它们对靶向致癌G4 DNA的影响。生物物理、生化和计算评估表明，具有优化接头的GL-Os即使在热或结构应力下也能增强与靶标G4的结合。值得注意的是，较长的接头拓宽了可靶向序列的范围，而不会引入空间位阻，从而提高了该平台在不同基因组环境中的适用性。这些发现确立了GL-Os作为一种强大而通用的工具，用于选择性靶向单个G4。通过促进对G4生物学的精确研究，这项工作为推进G4靶向治疗策略和探索它们在疾病背景中的作用奠定了基础。
