Catalytic hairpin assembly-based double-end DNAzyme cascade-feedback amplification for sensitive fluorescence detection of HIV-1 DNA

Liu, Xiaoyu; Zhou, Xiaomei; Xia, Xinyu; Xiang, Hua

doi:10.1016/j.aca.2019.10.051

Cited by 35 publications

(18 citation statements)

References 40 publications

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“…DNA-based feedback cascades can significantly enhance signal propagation for reactions where target DNA concentrations are low [2][3][4][5][6][7][8][9][10]; however, these feedback cascades have a tendency to be 'leaky'. Any small amount of circuit instability has the potential to be amplified into a large amount of nonspecific background signal [11][12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

Hasick

Lawrence²,

Ramadas³

et al. 2020

Molecules

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The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic Subzymes. These were individually tethered to microparticles (MP) and separated by a porous membrane rendering them unable to interact. In the presence of a target, active PlexZymes® cleave a first Subzyme, which separates a first DNAzyme from its MP, allowing the DNAzyme to migrate through the membrane, where it can cleave a second Subzyme. This releases a second DNAzyme which can now migrate through the membrane and cleave more of the first Subzyme, thus initiating a cross-catalytic cascade. Activated DNAzymes can additionally cleave fluorescent substrates, generating a signal, and thereby, indicating the presence of the target. The method detected 1 fM of DNA homologous to the ompA gene of Chlamydia trachomatis within 30 min, demonstrating a 10,000-fold increase in sensitivity over PlexZyme detection alone. The Subzyme cascade is universal and can be triggered by any target by modifying the target sensing arms of the PlexZymes. Further, it is isothermal, protein-enzyme-free and shows great potential for rapid and affordable biomarker detection.

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Section: Introductionmentioning

confidence: 99%

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

Hasick

Lawrence²,

Ramadas³

et al. 2020

Molecules

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“…At present, common DNA detection methods include southern blot hybridization, [1,2] electrochemiluminescence, [3] electrochemical, [4,5] colorimetric, [6] resonance light scattering [7] , and so on. To increase the detection sensitivity, these detection methods are combined with various signal amplification strategies such as loop-mediated isothermal amplification techniques, [8,9] catalytic DNA hairpin assembly, [10][11][12] DNA walker, [13,14] strand displacement amplification reactions, [15,16] and rolling circle amplification. [17] Among them, the combination of electrochemical sensors and DNA walkers has become a hot topic of current research due to their good programmability, ultra-high sensitivity, and excellent biocompatibility.…”

Section: Introductionmentioning

confidence: 99%

A sensitive electrochemical DNA sensor based on reduced graphene oxide modified electrode

Shu

et al. 2022

J Chinese Chemical Soc

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In this work, an electrochemical sensing platform, analogous to a DNA walker, was explored with exonuclease III (EXO III) as a driving force, tetraferrocene as a signal marker, and reduced graphene oxide (RGO) electrode as twodimensional (2D) orbit to realize ultrasensitive detection of target DNA. We designed a single hairpin DNA probe with 3 0 -end modified tetraferrocene, immobilized on the electrode surface by π-π stacking between the 5 0 terminus and reduced graphene oxide. In addition, EXO III digested the double-stranded DNA with a blunt 3 0 terminus formed by the target DNA and the probe DNA, thus degrading the 3 0 end of probe DNA, and resulting in the away movement of tetraferrocene from the electrode surface, decreasing the electrochemical signal. The proposed electrochemical sensor was very simple and stable with acceptable reproducibility, excellent DNA detection performance, and a detection limit as low as 0.3 pM.

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“…During the hybridization process, the target DNA is spontaneously released from the hairpin complex, allowing it to induce more hairpin opening and assembly events. The hairpin complexes combine with detection techniques like fluorescent [ [17] , [18] , [19] , [20] ], colorimetric [ [21] , [22] , [23] ], or electrochemical [ [24] , [25] , [26] ] sensors to improve the signal amplification and transduction of the target DNA, thereby enhancing the detection of very low abundance target DNA.…”

Section: Introductionmentioning

confidence: 99%

Catalytic hairpin DNA assembly-based chemiluminescent assay for the detection of short SARS-CoV-2 target cDNA

Yoon

Jeong

Hong

2021

Talanta

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Colorimetric sensors are recognized as a promising means for target molecule detection as they provide rapid, cost-effective, and facile sensing visible to the naked eye. Challenges remain though in terms of their detection sensitivity and specificity for short-length target genes. Herein, we demonstrate the successful combination of the catalytic hairpin DNA assembly (CHA) approach with enzyme-linked immunosorbent assay (ELISA)-mimicking techniques for a simple, sensitive, and sequence-specific colorimetric assay to detect short SARS-CoV-2 target cDNA. In the developed CHA-based chemiluminescent assay, a low concentration of target cDNA is continuously recycled to amplify dimeric DNA probes from two biotinylated hairpin DNA until the hairpin DNA is completely consumed. The dimeric DNA probes are effectively immobilized in a neutravidin-coated microplate well and then capture neutravidin-conjugated horseradish peroxidase via biotin-neutravidin interactions, resulting in a sensitive and selective colorless-to-blue color change. The developed sensing system exhibits a high sensitivity with a detection limit of ∼ 1 nM for target cDNA as well as the ability to precisely distinguish a single-base mismatched mutant gene within two hours. As the proposed system does not require complex protocols or expensive equipment to amplify target cDNA, it has the potential to be utilized as a powerful tool to improve the detection sensitivity of target genes for clinical diagnostics with colorimetric detection.

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Catalytic hairpin assembly-based double-end DNAzyme cascade-feedback amplification for sensitive fluorescence detection of HIV-1 DNA

Cited by 35 publications

References 40 publications

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

A sensitive electrochemical DNA sensor based on reduced graphene oxide modified electrode

Catalytic hairpin DNA assembly-based chemiluminescent assay for the detection of short SARS-CoV-2 target cDNA

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