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High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker

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Abstract

After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL−1, with a low detection limit of 2 CFU mL−1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine  C. sakazakii in real samples with recoveries of 92.86%—108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.

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The data that support the findings of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

This work was partly funded by the National Natural Science Foundation of China (32372423, 3221101215), the National Key Research and Development Program of China (2021YFE0101800), the S&T Plan Project of Jiangsu Provincial (BE2022324), the National First-class Discipline Program of Food Science and Technology (JUFSTR20180303), and Jiangsu Specially-Appointed Professor Program.

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Authors and Affiliations

  1. State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China

    Ningru Yang, Ning Ding, Shuo Qi, Zixuan Shang, Pengfei Ma, Imran Mahmood Khan, Zhouping Wang & Yu Xia

  2. College of Ocean Food and Biological Engineering, Jimmie University, Jimei University, Jimei District, Xiamen City, 361021, Fujian Province, China

    Imran Mahmood Khan

  3. Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China

    Zhouping Wang & Yin Zhang

  4. Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Lili Zhang

  5. Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China

    Zhouping Wang

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  1. Ningru Yang
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Yang, N., Ding, N., Qi, S. et al. High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker. Microchim Acta 191, 130 (2024). https://doi.org/10.1007/s00604-024-06199-2

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