CRISPR/Cas systems accelerating the development of aptasensors

Zhu, Chao; Zhang, Fan; Li, Huidong; Chen, Zilei; Yan, Mengmeng; Li, Linsen; Qu, Feng

doi:10.1016/j.trac.2022.116775

Cited by 8 publications

(6 citation statements)

References 146 publications

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“…Based on the programmability of nucleic acids, DNA logic circuits can interact with aptamers, specific binding trigger sequences, CRISPR-Cas systems, and various functional proteins to achieve recognition, capture, and discrimination of various target types. [60][61][62] The design principles of DNA logic circuits are rooted in DNA logic gates, which are characterized by probe recognition, conformational changes, information transmission, and in situ amplification. Built upon this foundation, DNA logic circuits integrate multiple different logic gate signals to form a logical information cascade with synchronized output.…”

Section: Dna Programming In Biomedical Fieldmentioning

confidence: 99%

“…The results are then effectively interpreted using Boolean logic, enabling the intelligent integration of the clinical test procedure and results. Based on the programmability of nucleic acids, DNA logic circuits can interact with aptamers, specific binding trigger sequences, CRISPR‐Cas systems, and various functional proteins to achieve recognition, capture, and discrimination of various target types 60–62 . The design principles of DNA logic circuits are rooted in DNA logic gates, which are characterized by probe recognition, conformational changes, information transmission, and in situ amplification.…”

Section: Dna Programming In Biomedical Fieldmentioning

confidence: 99%

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DNA logic programming: From concept to construction

Zhang,

Hu,

et al. 2023

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DNA programming, which is based on the principle of base complementary pairing and Boolean operations, exhibits organizational structures and algorithms similar to those observed in machine language. Consequently, the practical implementation of DNA logic programming can be achieved through the utilization of programming techniques, enabling the discrimination and output generation. In recent years, DNA programming has witnessed a convergence with disciplines, such as life sciences, medicine, and other interdisciplinary areas, thereby giving rise to an advanced research system that yields valuable insights. This development has paved the way for multidisciplinary cutting‐edge research. Furthermore, the successful transition from conceptualization to the practical implementation of DNA programming has been accomplished. This review summarizes the recent advances in DNA logic programming within the biomedical fields, specifically emphasizing the conceptualization and execution of DNA logic programming constructs. The benefits and obstacles associated with the adoption of DNA programming in cutting‐edge research areas are also highlighted.

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Section: Dna Programming In Biomedical Fieldmentioning

confidence: 99%

Section: Dna Programming In Biomedical Fieldmentioning

confidence: 99%

DNA logic programming: From concept to construction

Zhang,

Hu,

et al. 2023

VIEW

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“…19−21,24−28 For small molecule detection, aptamers are often used as affinity ligands, and a majority of methods utilize a structure-switchable aptamer to regulate the activity of Cas12a responsive to target information. [23][24][25]28 In most cases, the single-stranded active DNA (acDNA) of Cas12a is locked by the aptamer, and only the presence of the target triggers the release of acDNA and activation of Cas12a. 28−30 Another typical signal-off pattern relies on a rationally designed ssDNA probe, which functions as both a Cas12a activator and a targetbinding ligand.…”

mentioning

confidence: 99%

“…In the past few years, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), identified as an adaptive immune mechanism in bacteria and archaea, have sparked a research upsurge in the field of biosensing technology. , Cas12a is a CRISPR RNA (crRNA)-guided enzyme, which can cleave target double-stranded DNA (dsDNA) or target single-stranded DNA (ssDNA) within a RuvC catalytic pocket upon its target DNA complementary to the preordered seed region in crRNA (termed cis-cleavage activity). − Particularly, the target DNA-activated Cas12a can indiscriminately cleave surrounding nonspecific ssDNA with high enzymatic efficiency (termed trans-cleavage activity). ,, This unique cleavage property of Cas12a has been widely deployed to construct a series of amplified detection platforms for the analysis of different targets. − ,− For small molecule detection, aptamers are often used as affinity ligands, and a majority of methods utilize a structure-switchable aptamer to regulate the activity of Cas12a responsive to target information. − , In most cases, the single-stranded active DNA (acDNA) of Cas12a is locked by the aptamer, and only the presence of the target triggers the release of acDNA and activation of Cas12a. − Another typical signal-off pattern relies on a rationally designed ssDNA probe, which functions as both a Cas12a activator and a target-binding ligand. Target binding directly inhibits acDNA-crRNA hybridization and Cas enzyme activation. , Because of the dearth of flexible signal transduction strategies, the current methods require rational engineering of acDNA and corresponding crRNA according to the target small molecule, limiting the application of the CRISPR/Cas system for the detection of a wide range of analytes.…”

mentioning

confidence: 99%

CRISPR/Cas12a-Amplified Aptamer Switch Microplate Assay for Small Molecules

Zhu,

Yu,

Zhao

2024

Anal. Chem.

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The presence of small molecule contaminants such as mycotoxins and heavy metals in foods and the environment causes a serious threat to human health and huge economic losses. The development of simple, rapid, sensitive, and on-site methods for small molecule pollutant detection is highly demanded. Here, combining the advantages of structure-switchable aptamer-mediated signal conversion and CRISPR/Cas12a-based signal amplification, we developed a CRISPR/Cas12a-amplified aptamer switch assay on a microplate for sensitive small molecule detection. In this assay, a short DNA strand complementary to the aptamer (cDNA) is immobilized on a microplate, which can capture the aptamer-linked active DNA probe (Apt-acDNA) in the sample solution when the target is absent. With the addition of the Cas12a reporter system, the captured Apt-acDNA probes activate Cas12a to indiscriminately cleave fluorescent DNA substrates, producing a high fluorescence signal. When the target is present, the Apt-acDNA probe specifically binds to the target rather than hybridizing with cDNA on the microplate, and the fluorescence signal is reduced. The analytical performance of our method was demonstrated by the detection of two highly toxic pollutants, aflatoxin B1 (AFB1) and cadmium ion (Cd2+), as examples. The assay exhibited good selectivity and high sensitivity, with detection limits of 31 pM AFB1 and 3.9 nM Cd2+. It also allowed the detection of targets in the actual sample matrix. With the general signal conversion strategy, this method can be used to detect other targets by simply changing the aptamer and cDNA, showing potential practical applications in broad fields.

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“…Similarly, Cas13a recognizes single-stranded RNA (ssRNA) and cleaves both the target sequence and the surrounding ssRNA. However, as the CRISPR system cannot directly recognize proteins or small molecules, it relies on signal transduction strategies to establish connections. − Chen et al presented an innovative signal-amplification-linked immunosorbent assay based on CRISPR/Cas13a for the ultralow-concentration detection of proteins . This approach employs the antigen–antibody interaction as the signal transduction mechanism.…”

mentioning

confidence: 99%

Programmable Aptasensor for Regulating CRISPR/Cas12a Activity

Yu,

Li,

Shi

et al. 2023

ACS Sens.

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CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA comprising the aptamer sequence, locker DNA, and a crRNA recognition region, forming a hairpin structure through complementary hybridization. With T4 DNA polymerase, the crRNA recognition region was transformed into a complete double-stranded DNA through stem-loop extension, thereby activating the trans-cleavage activity of Cas 12a and generating fluorescence signals. The specific binding between the target molecule and aptamer disrupted the formation of the hairpin structure, altering the fluorescence signals. Notably, the CPAS platform allows for easy customization by simply changing the aptamer sequence and locker DNA, without entailing adjustments to the crRNA. The optimal number of bases in the locker DNA was determined to be seven nucleotides for the SARS-CoV-2 spike (S) protein and four nucleotides for ATP. The CPAS platform exhibited high sensitivity for S protein and ATP detection. Integration with a lateral flow assay enabled sensitive detection within 1 h, revealing its excellent potential for portable analysis.

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CRISPR/Cas systems accelerating the development of aptasensors

Cited by 8 publications

References 146 publications

DNA logic programming: From concept to construction

DNA logic programming: From concept to construction

CRISPR/Cas12a-Amplified Aptamer Switch Microplate Assay for Small Molecules

Programmable Aptasensor for Regulating CRISPR/Cas12a Activity

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