Virtual screening and site-directed mutagenesis-derived aptamers for precise <i>Salmonella typhimurium</i> prediction: emphasizing OmpD targeting and G-quadruplex stability

The efficient detection of the foodborne pathogen <i>Salmonella typhimurium</i> has historically been hampered by the constraints of traditional methods, characterized by protracted culture periods and intricate DNA extraction processes for PCR. To address this, our research innovatively focuses on the crucial and relatively uncharted virulence factor, the Outer Membrane Protein D (OmpD) in <i>Salmonella typhimurium</i>. By harmoniously integrating the power of virtual screening and site-directed mutagenesis, we unveiled aptamers exhibiting marked specificity for OmpD. Among these, aptamer 7ZQS stands out with its heightened binding affinity. Capitalizing on this foundation, we further engineered a repertoire of mutant aptamers, wherein APT6 distinguished itself, reflecting unmatched stability and specificity. Our rigorous validation, underpinned by cutting-edge bioinformatics tools, amplifies the prowess of APT6 in discerning and binding OmpD across an array of <i>Salmonella typhimurium</i> strains. This study illuminates a transformative approach to the prompt and accurate detection of <i>Salmonella typhimurium</i>, potentially redefining boundaries in applied analytical chemistry and bolstering diagnostic precision across diverse research and clinical domains.

长期以来，食源性致病菌鼠伤寒沙门氏菌（Salmonella typhimurium）的高效检测一直受限于传统检测方法的诸多弊端：传统方法不仅需要漫长的培养周期，且PCR检测环节需开展复杂的DNA提取流程。针对上述问题，本研究创新性地聚焦于鼠伤寒沙门氏菌中一种关键且此前鲜有研究的毒力因子——外膜蛋白D（Outer Membrane Protein D，OmpD）。本研究通过融合虚拟筛选与定点突变技术的优势，成功筛选得到对OmpD具有显著特异性的适配体；其中，7ZQS适配体展现出更优的结合亲和力。在此基础上，本研究进一步构建了一系列突变适配体，其中APT6表现最为突出，具备无可比拟的稳定性与特异性。本研究依托前沿生物信息学工具开展了严格的验证实验，进一步证实APT6可在多种鼠伤寒沙门氏菌菌株中精准识别并结合OmpD。本研究为鼠伤寒沙门氏菌的快速精准检测提供了一种颠覆性策略，有望重塑应用分析化学领域的研究边界，并提升各类研究与临床场景中的诊断精准度。