基于计算机模拟技术优化筛选核酸适配体的初探

目的:通过分子模拟技术优化筛选5’单磷酸腺苷(AMP)的高特异性适配体,利用胶体金可视化试验验证筛选结果。方法:研究文献中已知的AMP原始适配体(S0)的结合位点,对7个关键碱基进行多轮迭代单点突变,获得新的适配体,进一步比较结合自由能,优化获得特异性高的适配体序列。结果:历经5轮筛选,优化筛选出4个特异性高的新序列(S1-S4),使用胶体金的可视化检测对最佳新序列(S4)和原始序列(S0)作比较,结果发现试验结果与模拟结果一致性良好。结论:计算机模拟技术优化筛选适配体具有省时、易制备、分子质量小、储存运输简单等多种优势,为快速获得特异性适配体提供了一个新方法、新思路。

Studies on Optimal Screening of Aptamer Based on Computer-aided Modeling

Aptamer has been applied for detection,separation/purification and clinic fields,because of many advantages such as stability,easy preparation,small molecular weight,simple storage and transportation.The traditional screening method always need complicated procedure and operation,and the mechanism of screening is still unclear.In the paper,based on computer-aided molecular modeling,the binding site of the known aptamer and 5'adenosine monophosphate(AMP)was studied,seven key bases were chosen to further mutate by wheel iteration orientation method.The new sequences were obtained by the comparation of the binding free energy step by step.After the fourth step,there were four new sequences(named as S1-S4)with high specificity were chosen.In the experiment,the best sequence(S4)and the initial sequence(S0)were identified by visual detection using colloidal gold.It was found that the experimental results were well agreement with the modeling results.It provides a basic platform to the optimal screening of the aptamer.