Effect of molecular crowders on ligand binding kinetics with G-quadruplex DNA probed by fluorescence correlation spectroscopy.

IF 2.4 3区 化学 Q3 CHEMISTRY, ANALYTICAL Methods and Applications in Fluorescence Pub Date : 2024-07-26 DOI:10.1088/2050-6120/ad63f5
Parvez Alam, Ndege Simisi Clovis, Ajay Kumar Chand, Mohammad Firoz Khan, Sobhan Sen
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Abstract

Guanine-rich single-stranded DNA folds into G-quadruplex DNA (GqDNA) structures, which play crucial roles in various biological processes. These structures are also promising targets for ligands, potentially inducing antitumor effects. While thermodynamic parameters of ligand/DNA interactions are well-studied, the kinetics of ligand interaction with GqDNA, particularly in cell-like crowded environments, remain less explored. In this study, we investigate the impact of molecular crowding agents (glucose, sucrose, and ficoll 70) at physiologically relevant concentrations (20% w/v) on the association and dissociation rates of the benzophenoxazine-core based ligand, cresyl violet (CV), with human telomeric antiparallel-GqDNA. We utilized fluorescence correlation spectroscopy (FCS) along with other techniques. Our findings reveal that crowding agents decrease the binding affinity of CV to GqDNA, with the most significant effect-a nearly three-fold decrease-observed with ficoll 70. FCS measurements indicate that this decrease is primarily due to a viscosity-induced slowdown of ligand association in the crowded environment. Interestingly, dissociation rates remain largely unaffected by smaller crowders, with only small effect observed in presence of ficoll 70 due to direct but weak interaction between the ligand and ficoll. These results along with previously reported data provide valuable insights into ligand/GqDNA interactions in cellular contexts, suggesting a conserved mechanism of saccharide crowder influence, regardless of variations in GqDNA structure and ligand binding mode. This underscores the importance of considering crowding effects in the design and development of GqDNA-targeted drugs for potential cancer treatment.

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通过荧光相关光谱探测分子挤出器对配体与 G 型四联 DNA 结合动力学的影响。
富含鸟嘌呤的单链 DNA 折叠成 G-quadruplex DNA(GqDNA)结构,在各种生物过程中发挥着至关重要的作用。这些结构也是配体的潜在靶标,有可能诱导抗肿瘤效应。虽然配体/DNA 相互作用的热力学参数已被充分研究,但配体与 GqDNA 相互作用的动力学,尤其是在类似细胞的拥挤环境中的动力学,仍然较少被探索。在本研究中,我们研究了生理相关浓度(20% w/v)的分子拥挤剂(葡萄糖、蔗糖和ficoll 70)对以苯并吩噁嗪为核心的配体甲酚紫(CV)与人类端粒反平行-GqDNA的结合和解离速率的影响。我们使用了荧光相关光谱(FCS)和其他技术。我们的研究结果表明,拥挤剂会降低 CV 与 GqDNA 的结合亲和力,其中影响最大的是 ficoll 70--降低了近三倍。FCS 测量结果表明,这种降低主要是由于粘度导致配体在拥挤环境中的结合速度减慢。有趣的是,解离率在很大程度上不受较小拥挤物的影响,仅在存在 ficoll 70 的情况下观察到很小的影响,这是因为配体与 ficoll 之间存在直接但微弱的相互作用。这些结果与之前报道的数据一起,提供了细胞环境中配体/GqDNA相互作用的宝贵见解,表明无论 GqDNA 结构和配体结合模式如何变化,糖拥挤剂的影响机制是一致的。这凸显了在设计和开发用于治疗癌症的 GqDNA 靶向药物时考虑拥挤效应的重要性。
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来源期刊
Methods and Applications in Fluorescence
Methods and Applications in Fluorescence CHEMISTRY, ANALYTICALCHEMISTRY, PHYSICAL&n-CHEMISTRY, PHYSICAL
CiteScore
6.20
自引率
3.10%
发文量
60
期刊介绍: Methods and Applications in Fluorescence focuses on new developments in fluorescence spectroscopy, imaging, microscopy, fluorescent probes, labels and (nano)materials. It will feature both methods and advanced (bio)applications and accepts original research articles, reviews and technical notes.
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