Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Shi, Kai; Dou, Baoting; Yang, Jianmei; Yuan, Ruo; Xiang, Yun

doi:10.1016/j.bios.2016.08.056

Cited by 63 publications

(26 citation statements)

References 41 publications

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“…As a versatile SDA isothermal amplification technique, catalytic hairpin assembly (CHA) is an enzyme-free DNA circuit that relies on a thermodynamically driven entropy gain process to achieve signal amplification, possibly permitting exponential amplification of a target sequence in 15 min 34 - 36 . By combining CHA with other detection techniques such as colorimetry 37 , fluorescence 38 , electrochemistry 39 , 40 , chemiluminescence 41 , Raman spectroscopy, and surface plasmon resonance, miscellaneous CHAs platforms have been developed for miRNAs, metal ions 42 and protein molecular analysis 43 . However, these strategies are associated with complex nanoparticles and fluorescence labelling processes, time-consuming methods or expensive equipment.…”

Section: Introductionmentioning

confidence: 99%

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

et al. 2018

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As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification.Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process. In the present of target miRNA, the stem of the corresponding hairpin detection probe (HDP) will be unfolded and expose the concealed domain. The corresponding hairpin assistant probe (HAP) then replaces the hybridized target miRNA to form specific HDP/HAP complexes and releases miRNA based on thermodynamically driven entropy gain process, and the released miRNA triggers the next recycle to produce tremendous corresponding HDP/HAP complexes.Results: The results showed that the CHA gel assay can detect miRNA at fM levels and shows good capability of discriminating miRNA family members and base-mismatched miRNAs. It is able to analyze miRNAs extracted from cell lysates, which are consistent with the results of conventional polymerase chain reaction (PCR) method. Depending on the length of the designed hairpin probes, the CHA gel assay consisting of different hairpin probes effectively discriminated and simultaneously detected multiple miRNAs in homogenous solution and miRNAs extracted from cell lysates.Conclusion: The work highlights the practical use of a conventional gel electrophoresis for sensitive interesting nucleic acid sequences detection.

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Section: Introductionmentioning

confidence: 99%

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

et al. 2018

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“…Electrochemical signals (current, differential pulse voltammetry) of reactants possess electrocatalytic capability for H 2 O 2 or electron transfer. Electrochemical biosensors based on CHA are classified into four types: 1) hairpins synthesized with electroactive indicators (toluidine blue, methylene blue, streptavidin‐alkaline phosphatase); 2) horseradish peroxidases or peroxidase mimics (G‐quadruplex/hemin complex, PdNPs@Fe‐metal organic frameworks microcrystals) formed in the resultant products that generate signals; 3) modified nanoparticles (Au nanoparticles, Fe 3 O 4 /CeO 2 @Au magnetic nanoparticles, Ag nanoclusters, MoS 2 nanoflowers, Au@Pt nanospheres) covalently bound to CHA products to magnify currents; and 4) electrochemical indicators (Pb nanoparticles, methylene blue) intercalated into the backbone of CHA products to produce signal changes …”

Section: Characterization and Development Of Chamentioning

confidence: 99%

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Liu

Zhang

Xie

et al. 2019

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Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme‐free, high‐efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single‐stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in‐depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000‐fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

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“…Furthermore, SIEP can be used to functionalize nanoparticles, including DNA origami (Okholm, Aslan, Besenbacher, Dong, & Kjems, 2015), liposomes (Ruysschaert, Paquereau, Winterhalter, & Fournier, 2006) and gold nanoparticles (Wang et al, 2016) , with ssDNA. The template-free SIEP is useful for the fabrication of sensors that can detect nucleases (Chen, Xu, Ji, & He, 2017), DNA Wan et al, 2013;Wan et al, 2014), RNA (Tjong, Yu, Hucknall, & Chilkoti, 2013), metal ions (Mei et al, 2016), tumor biomarkers (Wang et al, 2016) and proteins (Shi, Dou, Yang, Yuan, & Xiang, 2017) . An early study by Tjong et al demonstrated a sensing platform to detect ssDNA by first immobilizing a capture oligonucleotide on a glass surface, followed by SIEP at the 3′ end of the detected and hybridized ssDNA (Fig.…”

Section: Tdt Catalyzed Polynucleotide Synthesis On Surfacesmentioning

confidence: 99%

Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase

Deshpande

Yang

Chilkoti

et al. 2019

Methods in Enzymology

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The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.

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Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Cited by 63 publications

References 41 publications

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase

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