A highly sensitive and selective fluoride sensor based on a riboswitch-regulated transcription coupled with CRISPR-Cas13a tandem reaction

Ma, Yuan; Mou, Quanbing; Yan, Peng; Yang, Zhenglin; Xiong, Ying; Yan, Deyue; Zhang, Chuan; Zhu, Xinyuan; Lu, Yi

doi:10.1039/d1sc03508h

Cited by 24 publications

(21 citation statements)

References 80 publications

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“…Apart from the above modes, it is worth noting that the short fragment in the middle can also be designed as a unit for signal output. By simply setting specific sequences in this domain, signal output strategies suitable for different scenarios can be realized, which may include assays using triplex-forming oligonucleotides, , CRISPR-Cas proteins, ,− or special reagents, , just to name a few.…”

Section: Resultsmentioning

confidence: 99%

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

Huang

Yao

et al. 2021

Anal. Chem.

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Signal amplification is critical to achieving sensitive biosensing, but complex strategies often bring problems like system instability, false positive, or narrow target spectrum. Here, a selfextending DNA-mediated isothermal amplification (SEIA) system with simple reaction components is introduced to achieve rapid, robust, and significant signal amplification. In SEIA, based on spontaneous refolding of specific DNA domains and using the previous generation product as a template, a DNA strand can extend continuously in an approximate exponential growth pattern, which was accurately predicted by our formula and well supported by AFM results. Based on a set of proof-of-concept experiments, it was proved that the SEIA system can output different signals and flexibly integrate various functional nucleic acids, which makes it suitable for different scenarios and realizes broad-spectrum target detection. Taking into account the advantages of simplicity, flexibility, and efficiency, the SEIA system as an independent signal amplification module will enrich the toolbox of biosensing design.

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Section: Resultsmentioning

confidence: 99%

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

Huang

Yao

et al. 2021

Anal. Chem.

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“…In 2016, Cas13a collateral cleavage activity was found (Abudayyeh et al., 2016), leading to the new era of CRISPR‐Cas‐based biosensors. With the first comprehensive and applicable system—SHERLOCK system—proposed in 2017 (Gootenberg et al., 2017), CRISPR‐Cas‐based detection became established and expanded continuously during the following years, which reflects a rapid development of this newly emerging technology (Bruch, Baaske, et al., 2019; Dai et al., 2019; de Puig, Lee, Najjar, Tan, Soeknsen, et al., 2021; Fozouni et al., 2021; Huang et al., 2018; Joung, Ladha, Saito, Kim, et al., 2020; Joung, Ladha, Saito, Segel, et al., 2020; Lee et al., 2021; Li et al., 2019; Li et al., 2018; Ma, Mou, et al., 2021; Teng et al., 2019; Tian et al., 2021; Zhou et al., 2018). In terms of building biosensors, CRISPR‐Cas exhibits tremendous potential for ultrasensitive and multiplexed detection with a much more rapid and precise measure (Bruch, Urban, et al., 2019).…”

Section: Crispr‐cas‐based Detectionmentioning

confidence: 99%

“…Note that green: Cas9‐based system; yellow: Cas12‐based system; blue: Cas13‐based system. [1] (Ishino et al., 1987); [2] (Jansen et al., 2002); [3] (Makarova et al., 2006); [4] (Barrangou et al., 2007); [5] (Jinek et al., 2012); [6] (Cong et al., 2013); [7] (Zetsche et al., 2015); [8] (Shmakov et al., 2015); [9] (Abudayyeh et al., 2016); [10] (Cyranoski, 2016); [11] (Pardee et al., 2016); [12] (Guk et al., 2017); [13] (Gootenberg et al., 2017); [14] (Li et al., 2018); [15] (Huang et al., 2018); [16] (Zhou et al., 2018); [17] (Gootenberg et al., 2018); [18] (Myhrvold et al., 2018); [19] (Chen et al., 2018); [20] (Stella et al., 2017); [21] (Teng et al., 2018); [22] (Harrington et al., 2018); [23] (Hajian et al., 2019); [24] (Liang et al., 2019); [25] (Dai et al., 2019); [26] (Teng et al., 2019); [27] (Li et al., 2019); [28] (Bruch, Baaske, et al., 2019); [29] (Peng, Zhou, Liu, et al, 2020); [30] (Zhou et al, 2020); [31] (Fozouni et al, 2021); [32] (Ackerman et al, 2020); [33] (Joung, Ladha, Saito, Segel, et al, 2020); [34] (Joung, Ladha, Saito, Kim, et al, 2020); [35] (Wang, Xiong, et al, 2020); [36] (Lee et al, 2021); [37] (Tian et al, 2021); [38] (Ma, Mou et al., 2021); [39] (Jiao et al, 2021); [40] (Zhang, Zhou, et al, 2021); [41] (de Puig, Lee, Najjar, Tan, Soekensen, et al, 2021)…”

Section: Crispr‐cas‐based Detectionmentioning

confidence: 99%

CRISPR‐Cas‐based detection for food safety problems: Current status, challenges, and opportunities

Man

Liu

2022

Comp Rev Food Sci Food Safe

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Food safety is one of the biggest public issues occurring around the world. Microbiological, chemical, and physical hazards can lead to food safety issues, which may occur at all stages of the supply chain. In order to tackle food safety issues and safeguard consumer health, rapid, accurate, specific, and field-deployable detection methods meeting diverse requirements are one of the imperative measures for food safety assurance. CRISPR-Cas system, a newly emerging technology, has been successfully repurposed in biosensing and has demonstrated huge potential to establish conceptually novel detection methods with high sensitivity and specificity. This review focuses on CRISPR-Cas-based detection and its current status and huge potential specifically for food safety inspection. We firstly illustrate the pending problems in food safety and summarize the popular detection methods. We then describe the potential applications of CRISPR-Casbased detection in food safety inspection. Finally, the challenges and futuristic

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“…[22] Produced transcripts can also be detected using Cas13a-based technology, further increasing detection sensitivity. [23,24] These new biosensors proved to be very efficient in aqueous solution, with a detection limit compatible with monitoring of drinking water. [8] Yet these systems rely on cell-free extracts or purified proteins, [22] and on expensive fluorogenic RNA analogues.…”

Section: Introductionmentioning

confidence: 99%

“…[8] Yet these systems rely on cell-free extracts or purified proteins, [22] and on expensive fluorogenic RNA analogues. [23,24] Moreover, such rather complex systems are efficient for highly sensitive single point measurements but less well-suited for direct analysis of fluoride and monitoring its production in solution.…”

Section: Introductionmentioning

confidence: 99%

FluorMango, an RNA‐Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

Husser

Vuilleumier

Ryckelynck

2022

Small

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an impressive level by riboswitches, a class of RNA motifs mostly found in the 5′ untranslated regions of some bacterial messenger RNAs (mRNAs). These sequences are able to specifically switch their structure in the presence of a target ligand, usually a small molecule, in order to control downstream gene expression (transcription or translation). [1][2][3][4] Riboswitches usually comprise two domains: a sensor aptamer that specifically recognizes a target molecule (with an affinity sometimes exceeding that of antibodies for their antigen), and a regulatory platform that remodels a region of the mRNA to modulate its transcription and/or its translation. The two domains are usually functionally connected by a transducing element, also called communication module. [1] Their modular structure makes riboswitches an excellent starting point for molecular engineering. For instance, exchanging the sensor aptamer domain for another one, natural or synthetic, already enabled the development of engineered riboswitches for application in living cells as well as in cell-free systems. [5][6][7] Thus, using such a construct to control the expression of a reporter gene (e.g., coding for a fluorescent protein, luciferase or another reporting enzyme), would yield a biosensor, that is, a biological molecule (or system) that converts the presence of a specific molecule into a measurable signal. [8] Among the wide palette of potential target ligands for this technology, small negatively charged molecules are expected to be the most difficult to target using RNA-based sensors as they offer only a low number of possible interaction sites and because strong electrostatic repulsion with polyanionic nucleic acids is anticipated. Fluoride, the smallest and the most electronegative anion, represents an extreme case in this context. However, its toxicity and often-problematic levels in drinking water make it a highly relevant target for specific detection. [9] Fluoride is also a potential degradation product of fluorinated compounds, an emerging class of persistent and toxic chemicals. [10] Specific detection of this ion would be useful in the development of high-throughput activity assays for the discovery of defluorination enzymes, of which only a few are currently known. [11] To be applicable, a corresponding sensor should be biocompatible, highly selective, easy to use, nontoxic, commercially available or easy to produce, and generate a fluorescent signal compatible with very high-throughput screening pipelines. [12] At present, fluoride is detectable by fluoride-specific electrodes [13,14] or colorimetry, [15,16] but none of these approaches fulfills all the above-mentioned requirements. Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid...

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A highly sensitive and selective fluoride sensor based on a riboswitch-regulated transcription coupled with CRISPR-Cas13a tandem reaction

Abstract: A fluoride sensor based on riboswitch-regulated transcription coupled with Cas13a sensor can detect fluoride in water with a portable fluorometer. This sensor expands nuclei acid sensors to an anion, with high sensitivity and selectivity against other common anions.

Cited by 24 publications

References 80 publications

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

CRISPR‐Cas‐based detection for food safety problems: Current status, challenges, and opportunities

FluorMango, an RNA‐Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

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