Background Aptamers, single-stranded DNAs or RNAs, can be selected from a library containing random sequences using a method called Systematic Evolution of Ligands by EXponential Enrichment (SELEX). In SELEX, monitoring the enriching statuses of aptamer candidates during the process is a key step until today. Conformational change of an aptamer caused by target-binding in gel can be used to indicate its statuses of binding. Results In this study, an easy-to-implement gel-based diffusion method (GBDM) was developed to monitor the interaction between enriched aptamer candidates and their targets. In order to prove the concept, characterization of aptamers targeting their targets including protein (thrombin) and non-protein molecules (acetamiprid, ATP, atrazine, profenofos and roxithromycin), respectively, were performed using mini gels. Our method has advantages over the common methods including easy performed with labor- and time- saving in experimental operation. The concept has been proven by monitoring enrichment of dynamic aptamer candidate libraries targeting a small molecule 2,2-bis(4-chlorophenyl) acetic acid (DDA) during SELEX process. A mini gel cassette was designed and fabricated by our laboratory to make mini agarose gels for diffusion with different directions. Conclusions These results indicate that GBDM, in particular, chasing diffusion is suitable for monitoring the interaction between enriched aptamer candidates and their targets. These pioneering efforts are helpful for novel aptamer selection by breaking through the technical bottleneck of aptamer development and helpful for development of novel aptasensors.

中文翻译：

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SELEX 工具：一种新颖且方便的基于凝胶的扩散方法，用于监测适体与靶标的结合。

背景 适配体、单链 DNA 或 RNA，可以使用称为通过指数富集的配体系统进化 (SELEX) 的方法从包含随机序列的文库中选择。在 SELEX 中，在此过程中监控候选适体的富集状态是直到今天的关键步骤。凝胶中由靶标结合引起的适体构象变化可用于指示其结合状态。结果 在本研究中，开发了一种易于实施的基于凝胶的扩散方法 (GBDM) 来监测富集的适体候选物与其靶标之间的相互作用。为了证明这一概念，分别使用微型凝胶对靶向其靶标的适体进行表征，包括蛋白质（凝血酶）和非蛋白质分子（啶虫脒、ATP、阿特拉津、丙溴磷和罗红霉素）。我们的方法与常用方法相比具有优势，包括在实验操作中易于执行、省力和省时。该概念已通过监测 SELEX 过程中针对小分子 2,2-双(4-氯苯基) 乙酸 (DDA) 的动态适体候选库的富集得到证实。我们实验室设计和制造了一个迷你凝胶盒，用于制作用于不同方向扩散的迷你琼脂糖凝胶。结论 这些结果表明，GBDM，特别是追逐扩散适用于监测富集的适体候选物与其靶标之间的相互作用。这些开创性的努力有助于突破适体开发的技术瓶颈，有助于新型适体的选择，有助于新型适体传感器的开发。