A dual amplification fluorescent strategy for sensitive detection of DNA methyltransferase activity based on strand displacement amplification and DNAzyme amplification

Cui, Wanling; Wang, Lei; Jiang, Wei

doi:10.1016/j.bios.2015.10.040

Cited by 39 publications

(18 citation statements)

References 28 publications

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“…24,143 SDA product detection is possible by methods such as gel electrophoresis, [144][145][146] molecular beacons 145,147 and fluorescence methods. [148][149][150] SDA has been applied in the diagnosis of tuberculosis through reverse-transcriptase SDA. 144 The technique which targeted alpha-antigen (85B protein) of Mycobacterium tuberculosis was successful at detecting and monitoring mRNA presence in patients undergoing tuberculosis treatment over 14 days, with an analytical sensitivity of 10 copies of target.…”

Section: Strand Displacement Amplification (Sda)mentioning

confidence: 99%

<p>Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections</p>

Obande

Singh

2020

IDR

120

115

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Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.

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Section: Strand Displacement Amplification (Sda)mentioning

confidence: 99%

<p>Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections</p>

Obande

Singh

2020

IDR

120

115

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“…25 However, the reported direct detection methods often suffer from poor sensitivity, 23−25 tedious preparation of nanomaterials, and fluorescence turn-off mode with the tendency of false positivity. 23−25 To enhance the sensitivity, strand displacement amplification reaction (SDA), 26,27 exonuclease/endonuclease nicking enzyme-assisted signal amplification, 28,29 rolling circle amplification (RCA), 30−32 duplex-specific nuclease-assisted amplification, 33 target-induced hyperbranched amplification, 34 exponential isothermal amplification reaction (EXPAR), 35,36 and hybridization chain reaction 37,38 are integrated with the fluorescence assay to detect DNA MTase activity. Despite the improved sensitivity, exonuclease/endonuclease-assisted signal amplification shows a high background signal resulting from nonspecific exonuclease III digestion and requires specific recognition sequences for nicking enzyme; 28,29 RCA, EXPAR, and SDA require the combination of a nicking enzyme and DNA polymerase, which may induce nonspecific amplification and false positivity.…”

Section: ■ Introductionmentioning

confidence: 99%

Construction of an APE1-Mediated Cascade Signal Amplification Platform for Homogeneously Sensitive and Rapid Measurement of DNA Methyltransferase in Escherichia coli Cells

et al. 2022

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DNA methylation is an essential genomic epigenetic behavior in both eukaryotes and prokaryotes. Deregulation of DNA methyltransferase (Dam MTase) can change the DNA methylation level and cause various diseases. Herein, we develop an apurinic/apyrimidinic endonuclease 1 (APE1)-mediated cascade signal amplification platform for homogeneously sensitive and rapid measurement of Dam MTase in Escherichia coli cells. This assay involves a partial double-stranded DNA (dsDNA) substrate and two hairpin signal probes (HP1 and HP2) that are modified with Cy5 and BHQ2 at two ends, respectively. When Dam MTase is present, it methylates the dsDNA substrate, and subsequently, endonuclease DpnI cleaves the methylated substrate, yielding trigger probe 1. Hybridization of trigger probe 1 with HP1 forms a partial dsDNA containing an apurinic/apyrimidinic (AP) site, which is cleaved by APE1 to induce the cyclic cleavage of HP1 and the production of abundant trigger probe 2. Subsequent hybridization of trigger probe 2 with HP2 forms a partial dsDNA with an AP site, inducing the cyclic cleavage of HP2 by APE1. Consequently, cyclic cleavage of HP1 and HP2 induces the generation of abundant Cy5 molecules, which are easily measured by single-molecule imaging. This assay can be performed homogeneously and rapidly within 2 h, which is the shortest among the reported amplification-based assays. Moreover, it exhibits good selectivity and high sensitivity, and it can discriminate Dam MTase from other enzymes and screen inhibitors. Importantly, it can accurately measure the Dam MTase activity in serum and E. coli cells, with promising applications in clinical diagnosis and drug discovery.

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“…It has been widely used in food safety, clinical diagnosis, and environmental monitoring because of its high specificity, easy in vitro synthesis and modification, etc . In recent years, the aptamer is usually combined with isothermal amplification to amplify the detecting signal of the target. − Also, researchers have tried to develop the cascade signal amplification strategy, achieving ultrasensitive detection. − RCA is often used as a part of cascade amplification due to its high specificity and strong amplification. − …”

Section: Introductionmentioning

confidence: 99%

Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification

Wang

Peng²,

Wu³

et al. 2021

Anal. Chem.

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17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA−RCA−MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836−183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8−107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.

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A dual amplification fluorescent strategy for sensitive detection of DNA methyltransferase activity based on strand displacement amplification and DNAzyme amplification

Cited by 39 publications

References 28 publications

<p>Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections</p>

<p>Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections</p>

Construction of an APE1-Mediated Cascade Signal Amplification Platform for Homogeneously Sensitive and Rapid Measurement of DNA Methyltransferase in Escherichia coli Cells

Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification

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