REVEALR: A Multicomponent XNAzyme-Based Nucleic Acid Detection System for SARS-CoV-2

Yang, Kefan; Chaput, John C.

doi:10.1021/jacs.1c02664

Cited by 75 publications

(79 citation statements)

References 17 publications

(32 reference statements)

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“…To facilitate this study, an artificial plasmid model was constructed to validate the methodology. Genes fragments (wild-SARS-CoV-2, mut-SARS-CoV-2, FluA, MERS, rhinovirus, and SARS-CoV-1) were cloned into TOPO vectors with a T7 primer, using a TOPO PCR cloning kit (Beijing, China) ( Table S1 ) [ 25 ]. The vectors were obtained via a TIANpure Midi Plasmid Kit (Tiangen Biotech Co, Ltd.).…”

Section: Methodsmentioning

confidence: 99%

Visualization of copper nanoclusters for SARS-CoV-2 Delta variant detection based on rational primers design

Zhu

2022

Talanta

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Here, based on the design of rational primers and copper nanoclusters (CuNCs), we present a method for the accurate detection of the SARS-CoV-2 Delta variant, which is capable of distinguishing the Delta variant with its single nucleotide polymorphism from the ‘wild type’ coronavirus (NC_045512.2), and realizing visualization signal out. Speciﬁcally, we show that dual priming oligonucleotide (DPO) primers and AT primers can be used to distinguish between wild types and mutations of this virus by polymerase chain reaction (PCR) analysis and that visualization can be achieved via the red fluorescence of CuNCs in ultraviolet radiation. Among the results, it was found that the R-1-down (DPO)-6I and F-1-30AT, with the single nucleotide deletion site designed at the 3′ end of the downstream primer, showed the best specificity towards the Delta variant. Moreover, the use of AT primers increased the AT contents of the PCR products, thus meeting the template requirements generated by the CuNCs. It was also found that the AT primers could assist with improving detection specificity. Finally, we demonstrate that the visualization of the CuNCs-based detection assay exhibited a linear relationship in 0.5 pg μL −1 –50 ng μL −1 , with a limit of quantitation (LOQ) of 0.5 pg μl −1 .

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Section: Methodsmentioning

confidence: 99%

Visualization of copper nanoclusters for SARS-CoV-2 Delta variant detection based on rational primers design

Zhu

2022

Talanta

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“…The developed X10-23 efficiently and persistently silenced gene activity via degradation of mRNA molecules in cultured mammalian cells. They also demonstrated the use of X10-23 to knock down allele-specific mRNA sequences in disease cells and to detect the viral pathogen responsible for COVID-19 with a detection limit of ≤20 aM [ 188 , 189 ]. To attain clear comprehension, a summary of the discussed nucleic-acid-based biosensors in this review is shown in Table 2 .…”

Section: Chemically Modified Nucleic Acid Analoguesmentioning

confidence: 99%

Nucleic Acids and Their Analogues for Biomedical Applications

Wang

Chu

et al. 2022

Biosensors

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Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.

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“…Among these, the commonly available are RNA-cleaved DNAzymes and G-quadruplex DNAzymes. Existing DNAzymes were used in current strategies for the detection and diagnosis of COVID-19 on a DNAzymes basis ( Tian et al, 2021 ; Yang and Chaput, 2021 ; Ahmad et al, 2021 ; Zhang et al, 2021a ). Although the selection of both aptamers and DNAzymes was done from ssDNA libraries, of which ssDNA libraries randomized and loaded up with RNA sequences serve for the selection of aptamers and DNAzymes, respectively.…”

Section: In Vitro Selection Of Functional Nucleic Acids Towards Understanding Covid-19mentioning

confidence: 99%

“… Detection Strategy Target Genes LOD Time Ref. Fluorescence Lateral flow readout S gene 20 aM 60 min Yang and Chaput (2021) RT-PCR Colorimetric readout N gene 1000 Copies of RNA ∼75 min Anantharaj et al (2020) RT-PCR Colorimetric readout N gene 100 Copies of RNA <1 h Ahmad et al (2021) Chemiluminescence Immunoassay SARS-CoV-2 antibodies 6.46 fg mL −1 ∼140 min ( Zhang et al, 2021a ) Logic DNA circuit Fluorescent nucleotide 3562–3581 and 32442–32461 of the COVID-19 complete genome 3.3 fM 75 min Pan et al (2021) Electrochemical N protein 8.33 pg mL −1 Unknown Tian et al (2021) …”

Section: Functional Nucleic Acid-based Diagnostic Strategies For Covid-19mentioning

confidence: 99%

“…XNAzyme, an artificial, catalytically active, multi-component nucleic-acid enzyme ( Taylor and Holliger, 2015 ), has modular properties and separation of input and output functions, with potential for integration into a variety of diagnostic biosensors ( Mokany et al, 2010 ). Yang et al ( Yang and Chaput, 2021 ) developed the RNA-Encoded Viral Nucleic Acid Analyte Reporter (REVEALR) on the basis of the novel discovery of XNAzyme 10–23 ( Fig. 5 D).…”

Section: Functional Nucleic Acid-based Diagnostic Strategies For Covid-19mentioning

confidence: 99%

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Functional nucleic acids as modular components against SARS-CoV-2: From diagnosis to therapeutics

Zhang

Liu

Zhang

2022

Biosensors and Bioelectronics

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Coronavirus Disease 2019 (COVID-19), which poses an extremely serious global impact on human public healthcare, represents a high transmission and disease-causing viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is expanding at a rapid pace. Therefore, it is urgent for researchers to establish effective platforms for the assay and treatment of SARS-CoV-2. Functional nucleic acids (FNAs), comprising aptamers and nucleases, are of primary concern within the biological and medical communities owing of the distinctive properties of their target recognition and catalysis. This review will concentrate on the essential aspects of insights regarding FNAs and their technological expertise for the diagnostic and therapeutic utilization against COVID-19. We first offer a historical perspective of the COVID-19 pandemics, its clinical characteristics and potential biomarkers. Then, we briefly discuss the current diagnostic and therapeutic methodology towards COVID-19, highlighting the superiorities and existing shortcomings. After that, we introduce the key features of FNAs, and summarize recent progress of in vitro selection of FNAs for SARS-CoV-2 specific proteins and RNAs, followed by highlighting the general concept of translating FNAs into functional probes for diagnostic and therapeutic purposes. Then, we critically review the emerging FNAs-based diagnostic and therapeutic strategies that are fast, precise, efficient, and highly specific to fight COVID-19. Finally, we identify remaining challenges and offer future outlook of this emerging field.

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REVEALR: A Multicomponent XNAzyme-Based Nucleic Acid Detection System for SARS-CoV-2

Cited by 75 publications

References 17 publications

Visualization of copper nanoclusters for SARS-CoV-2 Delta variant detection based on rational primers design

Visualization of copper nanoclusters for SARS-CoV-2 Delta variant detection based on rational primers design

Nucleic Acids and Their Analogues for Biomedical Applications

Functional nucleic acids as modular components against SARS-CoV-2: From diagnosis to therapeutics

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