College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China.
Molecules. 2022 Sep 5;27(17):5725. doi: 10.3390/molecules27175725.
The Systematic Evolution of Ligands by EXponential enrichment (SELEX) is conventionally an effective method to identify aptamers, which are oligonucleotide sequences with desired properties to recognize targets specifically and sensitively. However, there are some inherent limitations, e.g., the loss of potential high-affinity sequences during biased iterative PCR enrichment processes and the limited structural diversity of the initial library, which seriously restrict their real-world applications. To overcome these limitations, the in silico base mutagenesis post-SELEX strategy based on the low Gibbs free energy (ΔG) and genetic algorithm was developed for the optimization of the interferon-gamma aptamer (B1-4). In the process of evolution, new sequences were created and the aptamer candidates with low ΔG values and advanced structures were produced. After five rounds of selection, systematic studies revealed that the affinity of the newly developed evolutionary aptamer (M5-5) was roughly 10-fold higher than that of the parent aptamer (B1-4), and an aptasensor detection system with a limit-of-detection (LOD) value of 3.17 nM was established based on the evolutionary aptamer. The proposed approach provided an efficient strategy to improve the aptamer with low energy and a high binding ability, and the good analytical utility thereof.
指数富集配体系统进化（SELEX）通常是一种有效的方法来识别适体，即具有特定识别靶标特异性和敏感性所需性质的寡核苷酸序列。然而，存在一些固有限制，例如在偏向性迭代 PCR 富集过程中潜在高亲和力序列的丢失和初始文库结构多样性的限制，这严重限制了它们的实际应用。为了克服这些限制，开发了基于低吉布斯自由能（ΔG）和遗传算法的 SELEX 后计算机碱基诱变策略，用于优化干扰素-γ适体（B1-4）。在进化过程中，创建了新序列，并产生了具有低 ΔG 值和先进结构的适体候选物。经过五轮筛选，系统研究表明，新开发的进化适体（M5-5）的亲和力比母体适体（B1-4）高约 10 倍，并基于进化适体建立了具有检测限（LOD）值为 3.17 nM 的适体传感器检测系统。该方法提供了一种提高低能量和高结合能力适体的有效策略，以及良好的分析实用性。
