适体
化学
对接(动物)
荧光
纳米技术
组合化学
生物物理学
分子生物学
材料科学
量子力学
医学
生物
物理
护理部
作者
Yangzi Zhang,Longjiao Zhu,Xuan Ma,Shujin Zhu,Yongqiang Ma,Sabir Hussain,Xiaoyun He,Wentao Xu
标识
DOI:10.1021/acs.analchem.3c01194
摘要
The light-up aptamer-dimethylindole red (DIR) complexes have been applied in biochemistry analysis as promising signal transduction tools. However, the unfavorable repulsions between DIR and the long-sequence aptamer switch hinder the complex's further development, and it is urgent to engineer a feasible and efficient strategy for synchronously and rationally adjusting the DIR chemical structure and the DIR aptamer performance. Herein, we communicate a versatile docking-guided rational tailoring strategy to effectively upgrade a DNA aptamer which specifically turns on the fluorescence of a synthesized amino-functionalized DIR analogue (NH2-DIR). After optimizing with three-level tailoring strategies including molecule docking-guided tailoring, coarse tailoring, and fine tailoring, the NH2-DIR aptamer switch with higher binding affinity and specificity, considerable fluorescence-activation ability, and 40% shortened length was obtained. Integrating the experimental and docking results, the binding mechanism between NH2-DIR and the tailored aptamer was deciphered via three types of interactions.
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