Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food
Aptamers as a kind of biological recognition element have shown great potential in monitoring and the rapid quantification of organophosphorus pesticides (OPPs). However, molecules of OPPs are structurally similar and original aptamers selected by systematic evolution of ligands by exponential enric...
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| Format: | Article |
| Language: | English |
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Tsinghua University Press
2023-09-01
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| Series: | Food Science and Human Wellness |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213453023000332 |
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| author | Pengfei Chen Chaoqiong Hu Xuan Tao Zheng Zhou Lijun Wang Xiao Yang Zhenming Che Xianggui Chen Yukun Huang |
| author_facet | Pengfei Chen Chaoqiong Hu Xuan Tao Zheng Zhou Lijun Wang Xiao Yang Zhenming Che Xianggui Chen Yukun Huang |
| author_sort | Pengfei Chen |
| collection | DOAJ |
| description | Aptamers as a kind of biological recognition element have shown great potential in monitoring and the rapid quantification of organophosphorus pesticides (OPPs). However, molecules of OPPs are structurally similar and original aptamers selected by systematic evolution of ligands by exponential enrichment are usually long-chain bases, which hamper the further application under OPPs-aptamer recognition. The aim of the research was to develop a new strategy to design oligonucleotide sequences for binding OPPs by combination of experimental and molecular modeling methods. 3D models of aptamers binding OPPs were constructed, and binding energy and the most probable binding site for the OPPs were then determined by molecular docking, and the binding sites were further confirmed by the results of 2-AP replaced experiments. Based on the docking results, a new aptamer for detection 4 representative OPPs with only 29 bases was designed by reasonable truncation and mutation of the reported aptamer (named S4-29). The interaction between this new aptamer and OPPs were analyzed by molecular docking, microscale thermophoresis, circular dichroism and fluorometric analysis. The results revealed that the new aptamer exhibit more superior recognition performance to OPPs, which can be promote the monitoring ability of OPPs contaminations in food. |
| format | Article |
| id | doaj-art-cfa6d40255b741f6a033d770b16da3e1 |
| institution | Kabale University |
| issn | 2213-4530 |
| language | English |
| publishDate | 2023-09-01 |
| publisher | Tsinghua University Press |
| record_format | Article |
| series | Food Science and Human Wellness |
| spelling | doaj-art-cfa6d40255b741f6a033d770b16da3e12025-02-03T05:40:26ZengTsinghua University PressFood Science and Human Wellness2213-45302023-09-0112517081715Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in foodPengfei Chen0Chaoqiong Hu1Xuan Tao2Zheng Zhou3Lijun Wang4Xiao Yang5Zhenming Che6Xianggui Chen7Yukun Huang8Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, China; Chengdu Brilliant Pharmaceutical Co., Ltd., Chengdu 610041, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, China; Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, YibinXihua University Research Institute, Yibin 644004, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, China; Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, YibinXihua University Research Institute, Yibin 644004, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, ChinaChongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, China; Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, YibinXihua University Research Institute, Yibin 644004, China; Corresponding authors at: School of Food and Biological Engineering, Xihua University, Chengdu 610039, China.Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, School of Food and Biological Engineering, Xihua University, Chengdu 610039, China; Key Laboratory of Food Non-Thermal Processing, Engineering Technology Research Center of Food Non-Thermal Processing, YibinXihua University Research Institute, Yibin 644004, China; Corresponding authors at: School of Food and Biological Engineering, Xihua University, Chengdu 610039, China.Aptamers as a kind of biological recognition element have shown great potential in monitoring and the rapid quantification of organophosphorus pesticides (OPPs). However, molecules of OPPs are structurally similar and original aptamers selected by systematic evolution of ligands by exponential enrichment are usually long-chain bases, which hamper the further application under OPPs-aptamer recognition. The aim of the research was to develop a new strategy to design oligonucleotide sequences for binding OPPs by combination of experimental and molecular modeling methods. 3D models of aptamers binding OPPs were constructed, and binding energy and the most probable binding site for the OPPs were then determined by molecular docking, and the binding sites were further confirmed by the results of 2-AP replaced experiments. Based on the docking results, a new aptamer for detection 4 representative OPPs with only 29 bases was designed by reasonable truncation and mutation of the reported aptamer (named S4-29). The interaction between this new aptamer and OPPs were analyzed by molecular docking, microscale thermophoresis, circular dichroism and fluorometric analysis. The results revealed that the new aptamer exhibit more superior recognition performance to OPPs, which can be promote the monitoring ability of OPPs contaminations in food.http://www.sciencedirect.com/science/article/pii/S2213453023000332Organophosphorus pesticidesAptamerRecognition mechanismSequence optimization |
| spellingShingle | Pengfei Chen Chaoqiong Hu Xuan Tao Zheng Zhou Lijun Wang Xiao Yang Zhenming Che Xianggui Chen Yukun Huang Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food Food Science and Human Wellness Organophosphorus pesticides Aptamer Recognition mechanism Sequence optimization |
| title | Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| title_full | Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| title_fullStr | Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| title_full_unstemmed | Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| title_short | Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| title_sort | recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food |
| topic | Organophosphorus pesticides Aptamer Recognition mechanism Sequence optimization |
| url | http://www.sciencedirect.com/science/article/pii/S2213453023000332 |
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