A CRISPR-Cas12a-powered magnetic relaxation switching biosensor for the sensitive detection of Salmonella

Shen, Yafang; Jia, Fei; He, Yawen; Fu, Yingchun; Fang, Weihuan; Wang, Jianping; Li, Yanbin

doi:10.1016/j.bios.2022.114437

Cited by 35 publications

(11 citation statements)

References 38 publications

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“…Compared to traditional detection methods and CRISPR-based detection system (Jiang et al 2021; Ke et al 2022; Kralik and Ricchi 2017; Shen et al 2022; Tian et al 2022), we obtain the result by deep learning-assisted classification within a very short period of time (15ms for multiclass classification of one image) without bulky instruments. Besides, transfer learning is adapted for deep learning models and a maximum of 98.75% accuracy for multiclass classification is achieved ( Table 4 ).…”

Section: Discussionmentioning

confidence: 99%

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Lei

Lian

Zhang

et al. 2022

Preprint

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Frog virus 3 (FV3, genera Ranavirus, family Iridoviridae), a double-stranded DNA virus, results in irreparable damage to biodiversity and significant economic losses to aquaculture. Although the existing FV3 detection methods are of high sensitivity and specificity, the complex procedure and requirement of expensive instruments limit their practical implantation. Herein, we develop a fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for FV3. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, we achieve a limit of detection (LoD) of 100 aM (60.2 copies/μL) by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, we build a smartphone microscopy (SPM) and achieve an LoD of 10 aM within 40 minutes. Four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32 are detectable by the proposed system. In addition, we deploy deep learning models for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100% and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, RPA-CRISPR/Cas12a combined with a smartphone readout and artificial intelligence (AI) assisted classification shows great potential for FV3 detection. This integrated system holds great promise for POC detection of aquatic DNA pathogens.

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Section: Discussionmentioning

confidence: 99%

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Lei

Lian

Zhang

et al. 2022

Preprint

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“…[211] Various magnetic and nucleic acidfunctionalized biosensors have recently been fabricated with nucleic acid technology for different biomarker analyses. [166,168,212] MNPs can be applied to facilitate electrochemical responses by blocking access to the electrodes and making them conductive or conformational changing after coating. [169] Tavallaie et al presented an ultrasensitive electrochemical sensor employing Au-coated magnetic nanoparticles modified by DNA probes as dispersible electrodes for the analysis of miRNA-21 in whole blood.…”

Section: Magnetic-integrated Biomarker Sensingmentioning

confidence: 99%

Nucleic Acids Enabled‐Interfacial Engineering for Biomarker Sensing with Distance Constraint Effects

Wang

Tang

et al. 2023

Advanced Sensor Research

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Controlling the distance of molecular recognition and signal transduction at the nano-bio interface plays a vital role in sensing molecular interactions, which significantly impacts how a biomarker sensor performs in terms of sensitivity, specificity, detection threshold, and response time. However, conventional biosensing interfaces without the design of distance constraint show limited molecular interactions, hindering target accessibility and mass transport. Nuclei acid-enabled engineering of biosensing interfaces facilitates highly regulated orientation and programmable density control of biomolecules, providing an effective strategy to improve the performance of biosensing platforms for early diagnosis of diseases and regulation of cellular activities. This review summarizes the recent advances in nucleic acid-based engineering of biosensing interfaces from a unique perspective of distance constraint effects. The roles of structural nucleic acids in delicately programmed assemblies, functional nucleic acids in molecular recognition, and sensor reactions at well-controlled distances are highlighted. Then applications of advanced biosensing platforms with the effect of distance constraint are introduced. Finally, the current challenges and future directions for developing such biosensors that can compete effectively to meet the requirements of point-of-care testing are also discussed.

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“…In addition to the above example of Cas12a as a signal sensor, scientists are also working on other easier and more efficient methods. Shen et al also integrated magnetic nanoparticles with the system to detect Salmonella, which performed well in spiked chicken samples [ 55 ].…”

Section: In Vitro Pathogen Detection Based On the Crispr/cas Systemmentioning

confidence: 99%

Application of the CRISPR/Cas System in Pathogen Detection: A Review

Yuan

et al. 2022

Molecules

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Early and rapid diagnosis of pathogens is important for the prevention and control of epidemic disease. The polymerase chain reaction (PCR) technique requires expensive instrument control, a special test site, complex solution treatment steps and professional operation, which can limit its application in practice. The pathogen detection method based on the clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated protein (CRISPR/Cas) system is characterized by strong specificity, high sensitivity and convenience for detection, which is more suitable for practical applications. This article first reviews the CRISPR/Cas system, and then introduces the application of the two types of systems represented by Type II (cas9), Type V (cas12a, cas12b, cas14a) and Type VI (cas13a) in pathogen detection. Finally, challenges and prospects are proposed.

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A CRISPR-Cas12a-powered magnetic relaxation switching biosensor for the sensitive detection of Salmonella

Cited by 35 publications

References 38 publications

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Nucleic Acids Enabled‐Interfacial Engineering for Biomarker Sensing with Distance Constraint Effects

Application of the CRISPR/Cas System in Pathogen Detection: A Review

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