Ultrasensitive isothermal method to detect microRNA based on target-induced chain amplification reaction

Kim, Hyo Yong; Song, Jayeon; Park, Hyun Gyu

doi:10.1016/j.bios.2021.113048

Cited by 24 publications

(12 citation statements)

References 42 publications

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“…Additionally, we verified whether the TWJ could initiate the subsequent exponential amplification reaction by measuring the real-time fluorescence signals generated by SYBR Green I binding. As shown in Figure 1C, in the presence of the target, the fluorescence signal increased rapidly in a short time, while the fluorescence signal from the blank group without the target increased in a relatively long time due to the nonspecific amplification of the secondary structure of template and the binding between dual templates, [10][11][12][13]35 and also the transient binding of the primer and template. The nonspecific amplification of the template was evidenced in Figure S2, from which we could see that lane 8 only contains the template and lane 7 contains both template and primer, under the combined action of polymerase and endonuclease, showed the bands of dsDNA of template product and ssDNA product after a relatively long reaction time (40 min), but none were observed after a short reaction time of 10 min (lanes 4 and 5).…”

Section: Acs Sensorsmentioning

confidence: 99%

Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis

Chen,

Jiang,

et al. 2023

ACS Sens.

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Rapid and simple nucleic acid detection is significant for disease diagnosis and pathogen screening, especially under specific conditions. However, achieving highly sensitive and specific nucleic acid detection to meet the time and equipment demand remains technologically challenging. In this study, we proposed a magnetic separation enhanced colorimetry biosensor based on a toehold-containing three-way junction (TWJ) induced multiple isothermal exponential amplification and the CRISPR/ Cas14a (C-TEC) biosensor. The TWJ template was designed as a Y−X−Y structure. In the presence of the target, the formation of toehold-containing TWJ complex induced primer extension, leading to the generation of amplified single-stranded DNA; this amplified DNA could then bind to either the free TWJ template for EXPAR reaction or the toehold of the TWJ complex for toehold-mediated strand displacement, thereby enabling the recycling of the target. The amplification products could trigger CRISPR/Cas14a for efficient trans-cleavage and release the magnetically bound gold nanoparticle probes for colorimetry detection. Using Mycobacterium tuberculosis 16S rDNA as the target, the proposed C-TEC could detect 16S rDNA down to 50 fM by the naked eye and 20.71 fM by UV−vis detector at 520 nm within 90 min under optimal conditions. We successfully applied this biosensor to clinical isolates of Mycobacterium tuberculosis. In addition, the C-TEC biosensor also showed feasibility for the detection of RNA viruses. In conclusion, the proposed C-TEC is a convenient, fast, and versatile platform for visual detection of pathogen DNA/RNA and has potential clinical applications.

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Section: Acs Sensorsmentioning

confidence: 99%

Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis

Chen,

Jiang,

et al. 2023

ACS Sens.

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“…In recent years, some assay systems based on nucleic acid-mediated isothermal signal amplification techniques have attracted the increasing attention of researchers, such as loop-mediated isothermal amplification technology, EXO III-assisted target cycle amplification technology, exponential amplification technology, strand replacement amplification technology, − and rolling circle amplification technology. − However, exogenous enzymes involved in the enzyme-assisted signal amplification process increase the assay cost and require specific reaction conditions, which greatly limits their further applications in some circumstances. As a potential alternative to enzymatic amplification, the non-enzymatic nucleic acid-based signal amplification technology provides new clues for the sensitive detection of miRNAs in complicated environments .…”

mentioning

confidence: 99%

Nonenzymatic Autonomous Assembly of Cross-Linked Network Structures from Only Two Palindromic DNA Components for Intracellular Fluorescence Imaging of miRNAs

Zhang

Gao

et al. 2022

ACS Sens.

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The abnormal expression of miRNA-21 is often found in tumor specimens and cell lines, and thus, its specific detection is an urgent need for the diagnosis and effective therapy of cancers. In this contribution, we demonstrate a palindrome-based hybridization chain reaction (PHCR) upon the stimuli of a short oligonucleotide trigger to perform the autonomous assembly of cross-linked network structures (CNSs) for the amplification detection of miRNA-21 and sensitive fluorescence imaging of cancerous cells. The building blocks are only two palindromic hairpin-type DNA strands that are separately modified with different fluorophores (Cy3 and Cy5), which is easily combined with the catalytic hairpin assembly (CHA) technique that can further amplify the signal output. Utilizing the CHA−PHCR assay system, a small amount of miRNA-21 can activate many triggers via CHA and in turn induce the PHCR-based CNS assembly from more DNA building blocks, bringing Cy3 and Cy5 into close proximity to each other and generating ultrasensitive fluorescence resonance energy transfer signals. As a result, target miRNA can be quantitatively detected down to as low as 10 pM with high assay specificity. The coexisting nontarget miRNAs and other biomacromolecules do not interfere with signal transduction. The developed assay system is suitable for screening different expression levels of miRNA-21 in living cells by fluorescence imaging. The palindrome-based cross-linking assembly can enhance the intracellular stability of assembled nanostructures by at least fivefold and exhibit the good universality for the detection of other miRNAs. Moreover, cancerous cells can be distinguished from healthy cells, and the CHA−PHCR assay is in good accordance with the gold standard PCR method, indicating a promising platform for the diagnosis of human cancers and other genetic diseases.

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“…MiRNAs represent a class of small noncoding RNAs (18–25 nucleotides) involved in posttranscriptional regulation of gene expression . Because the abnormal expression of miRNAs is closely associated with various diseases including cancers, neuronal or heart diseases, and diabetes, miRNAs have received great attention as attractive biomarkers for human diseases. − Recent studies also report that miRNAs are present in bodily fluids such as blood, saliva, and urine, making them promising targets for liquid biopsy. , To fully leverage the clinical value of miRNAs for the diagnosis and prognosis of human diseases, accurate identification and quantification of the miRNAs are imperative, but their small size and low abundance in addition to the sequence homology within same miRNA families makes this quite demanding. − …”

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confidence: 99%

Polychromatic Quantum Dot Array to Compose a Community Signal Ensemble for Multiplexed miRNA Detection

et al. 2022

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We herein describe a polychromatic quantum dot array (PQDA) to compose a community signal ensemble enabling accurate and precise quantification of miRNAs in a multiplexed manner. Advanced multicomponent ultrahigh-resolution patterning technique achieved by capsulation-assisted transfer printing following self-assembly-based poly(methyl methacrylate) (PMMA) patterning is utilized to manufacture the PQDA, which is designed to discharge a target miRNAs-specific set of fluorescent quantum dots (QDs) through the activity of duplex-specific nuclease (DSN). On the basis of the community signal ensemble produced by the discharged QD profiles, target miRNAs are very specifically identified down to a femtomolar level (1.27 fM) in a multiplexed manner over a wide dynamic range of up to 6 orders of magnitude. The practical diagnostic capability of this strategy is also demonstrated by reliably identifying breast cancer-specific miRNAs from heterogeneous cancer cell lysates.

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Ultrasensitive isothermal method to detect microRNA based on target-induced chain amplification reaction

Cited by 24 publications

References 42 publications

Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis

Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis

Nonenzymatic Autonomous Assembly of Cross-Linked Network Structures from Only Two Palindromic DNA Components for Intracellular Fluorescence Imaging of miRNAs

Polychromatic Quantum Dot Array to Compose a Community Signal Ensemble for Multiplexed miRNA Detection

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