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Wan F, Chen ZW, Xu TT, Guan JJ, Cui XM, Kang CZ, Zhou T, Wang CX, Guo LP, Yang Y. Selection and application of aptamers for p-hydroxybenzyl hydrogen sulfite after Gastrodia elata Bl. fumigated with sulfur. Talanta 2024; 269:125461. [PMID: 38056416 DOI: 10.1016/j.talanta.2023.125461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/01/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Gastrodia elata Bl. is a widely used traditional Chinese medicine known for its medicinal properties. However, during the drying process, G. elata is often fumigated with sulfur to prevent corrosion and improve its appearance. Sulfur-fumigation can result in a reduction in the effective components of the herb and can also be hazardous to human health due to the remaining sulfur dioxide. Sulfur-fumigation of G. elata poses a significant challenge to both end-users and researchers. The detection of p-hydroxybenzyl hydrogen sulfite (p-HS) is a useful tool in determining whether G. elata has been fumigated with sulfur. Unfortunately, the current method for detecting p-HS is costly and requires sophisticated instruments. Therefore, there is a need to develop a more cost-effective and user-friendly method for the detection of p-HS. This study utilized the Capture-SELEX technique to screen high-affinity aptamers for p-HS, which were subsequently characterized by isothermal titration calorimetry (ITC). An aptamer sequence (seq 6) with a high affinity of Kd = 26.5 μM was obtained following 8 rounds of selection against p-HS. With the aptamer serving as the recognition element and gold nanoparticles as the colorimetric indicator, a simple and efficient colorimetric sensor was developed for the specific detection of p-HS. This detection method exhibited a limit of detection of 1 μg/ml, while the p-HS recoveries demonstrated a range of between 88.5 % and 105 % for samples of G. elata obtained in the market. In summary, the aptamer exhibited a high affinity for p-HS, and the sensor developed through the use of a colloidal gold detector based on nucleic acid aptamer can be utilized for rapid detection of sulfur-fumigated G. elata. With these findings, this research paper provides valuable scientific insights and highlights significant potential for future studies in this area.
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Affiliation(s)
- Fen Wan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Zhuo-Wen Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Ting-Ting Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Jin-Jie Guan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Xiu-Ming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, China
| | - Chuan-Zhi Kang
- China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tao Zhou
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Cheng-Xiao Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, China
| | - Lan-Ping Guo
- China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Ye Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China; Yunnan Provincial Key Laboratory of Panax Notoginseng, Kunming, 650500, China.
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Chen L, Zhang B, Wu Z, Liu G, Li W, Tang Y. In Silico discovery of aptamers with an enhanced library design strategy. Comput Struct Biotechnol J 2023; 21:1005-1013. [PMID: 36733700 PMCID: PMC9883144 DOI: 10.1016/j.csbj.2023.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
With advances in force fields and algorithms, robust tools have been developed for molecular simulation of three-dimensional structures of nucleic acids and investigation of aptamer-target interactions. The traditional aptamer discovery technique, Systematic Evolution of Ligands by EXponential enrichment (SELEX), continues to suffer from high investment and low return, while in vitro screening by simulated SELEX remains a challenging task, where more accurate structural modeling and enhanced sampling limit the large-scale application of the method. Here, we proposed a modified aptamer enhanced library design strategy to facilitate the screening of target-binding aptamers. In this strategy, a comprehensive analysis of the original complexes and the target secondary structure were used to construct an enhanced initial library for screening. Our enhanced sequence library design strategy based on the target secondary structure explored a certain sequence space while ensuring the accuracy of the structural conformation and the calculation method. In an enhanced library of only a few dozen sequences, four sequences showed a similar or better binding free energy than the original aptamer, with consistently high binding stability over three rounds of multi-timescale simulations, ranging from - 30.27 to - 32.25 kcal/mol. Consequently, the enhanced library strategy based on the target secondary structure is shown to have very significant potential as a new aptamer design and optimization strategy.
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In silico approach for Post-SELEX DNA aptamers: A mini-review. J Mol Graph Model 2021; 105:107872. [PMID: 33765525 DOI: 10.1016/j.jmgm.2021.107872] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.
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WANG ZJ, CHEN EN, YANG G, ZHAO XY, QU F. Research Advances of Aptamers Selection for Small Molecule Targets. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60013-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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