Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N-acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico, and analyzed factors contributing to their binding affinities. Based on the findings, a novel binding mechanism was proposed, highlighting the central role of the stem structure of the aptamer in binding and recognizing GlySMs and the auxiliary role of the mismatched bases in the adjacent loop. Guided by this binding mechanism, an aptamer with a higher 6′-sialyllactose binding affinity was designed, achieving a K_D value of 4.54 ± 0.64 μM in vitro through a single shear and one mutation. The binding mechanism offers crucial guidance for designing high-affinity aptamers, enhancing the virtual screening efficiency for GlySMs. This streamlined workflow filters out ineffective binding sites, accelerating aptamer development and providing novel insights into glycan–nucleic acid interactions.

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ssDNA 适体针对含糖苷键小分子的结合机制的计算机模拟研究

基于适体的针对糖复合物的检测因其在识别各种疾病不同阶段糖的结构变化方面的巨大潜力而​​引起了广泛关注。然而，筛选含有高度灵活和多样化糖苷键的小碳水化合物或糖复合物的适体的挑战阻碍了它们的应用和商业化。在本研究中，我们通过计算机研究了三种含糖苷键的小分子（GlySM；葡萄糖、N-乙酰神经氨酸和新霉素）与其相应适体之间的结合构象，并分析了影响其结合亲和力的因素。基于这些发现，提出了一种新的结合机制，强调了适配体茎结构在结合和识别GlySM中的核心作用以及相邻环中错配碱基的辅助作用。以此结合机制为指导，设计了一种具有更高6'-唾液酸乳糖结合亲和力的核酸适配体，通过一次剪切和一次突变，在体外获得了4.54±0.64μM的K _D值。该结合机制为设计高亲和力适体提供了重要指导，提高了 GlySM 的虚拟筛选效率。这种简化的工作流程可以过滤掉无效的结合位点，加速适体的开发，并为聚糖-核酸相互作用提供新的见解。