Department of Plant Protection, College of Agricultural Sciences & Engineering, University of Tehran, Karaj, 31587-77871, Iran; Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, 3135933151, Karaj, Iran.
Department of Chemistry and NIS Interdepartmental Center, University of Turin, Via Pietro Giuria 5, 7, 10125, Turin, Italy; Department of Chemistry, University of Turin, Via Giuria, 5, I-10125, Turin, Italy.
Anal Chim Acta. 2020 Apr 8;1105:178-186. doi: 10.1016/j.aca.2020.01.045. Epub 2020 Jan 24.
A high affinity and selectivity DNA aptamer for aflatoxin B (AFB) was designed through Genetic Algorithm (GA) based in silico maturation (ISM) strategy. The sequence of a known AFB aptamer (Patent: PCT/CA2010/001292, Apt1) applied as a probe in many aptasensors was modified using seven GA rounds to generate an initial library and three different generations of ss DNA oligonucleotides as new candidate aptamers. Molecular docking methodology was used to screen and analyze the best aptamer-AFB complexes. Also, a new pipeline was proposed to faithfully predict the tertiary structure of all single stranded DNA sequences. By the second generation, aptamer Apt1 sequence was optimized in the local search space and five aptamers including F20, g12, C52, C32 and H1 were identified as the best aptamers for AFB. The selected aptamers were applied as probes in an unmodified gold nanoparticles-based aptasensor to evaluate their binding affinity to AFB and their selectivity against other mycotoxins (aflatoxins B, G, G, M, ochratoxin A and zearalenone). In addition, a novel direct fluorescent anisotropy aptamer assay was developed to confirm the binding interaction of the selected aptamers over AFB The ISM allowed the identification of an aptamer, F20, with up to 9.4 and 2 fold improvement in affinity and selectivity compared to the parent aptamer, respectively.
通过基于遗传算法（GA）的计算机模拟成熟（ISM）策略，设计了一种对黄曲霉毒素 B（AFB）具有高亲和力和选择性的 DNA 适体。将一种已知的 AFB 适体（专利：PCT/CA2010/001292，Apt1）的序列用作许多适体传感器中的探针，经过七轮 GA 修饰生成初始文库和三代 ssDNA 寡核苷酸作为新的候选适体。分子对接方法学用于筛选和分析最佳适体-AFB 复合物。此外，还提出了一种新的流水线来忠实地预测所有单链 DNA 序列的三级结构。在第二代，适体 Apt1 序列在局部搜索空间中进行了优化，鉴定了包括 F20、g12、C52、C32 和 H1 在内的五个适体作为 AFB 的最佳适体。所选适体被用作探针应用于未经修饰的基于金纳米粒子的适体传感器中，以评估它们与 AFB 的结合亲和力及其对其他霉菌毒素（黄曲霉毒素 B、G、G、M、赭曲霉毒素 A 和玉米赤霉烯酮）的选择性。此外，还开发了一种新颖的直接荧光各向异性适体测定法，以确认所选适体与 AFB 的结合相互作用。ISM 允许鉴定一种适体 F20，与亲本适体相比，其亲和力和选择性分别提高了 9.4 倍和 2 倍。
