DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins

Peng, Hanyong; Newbigging, Ashley M.; Wang, Zhixin; Tao, Jeffrey; Deng, Wenchan; Le, X. Chris; Zhang, Hongquan

doi:10.1021/acs.analchem.7b04926

Cited by 194 publications

(98 citation statements)

References 208 publications

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“…DNAzymes can be coupled with DNA amplification techniques for boosting sensitivity. Some common methods include protein enzyme-assisted (e.g., RCA and exonuclease III-based amplification) and enzyme-free mechanisms (e.g., hybridization chain reaction and catalytic hairpin assembly [CHA]) (Peng et al, 2018). For example, Li and coworkers coupled an E. coli-specific DNAzyme with RCA to achieve E. coli detection ( Figure 10A) (Liu et al, 2016).…”

Section: Applications In Signal Amplification Smart Materials Assembmentioning

confidence: 99%

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

Liu

2020

iScience

130

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Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.

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Section: Applications In Signal Amplification Smart Materials Assembmentioning

confidence: 99%

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

Liu

2020

iScience

130

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“…Thus, it is not surprising that significant effort has gone into engineering non-enzymatic DNA amplifier circuits that can detect and amplify nucleic acid signals based on strand-displacement mechanisms [15]. Examples of DNA amplifiers include entropy driven catalytic circuits [16], hybridization chain reactions [17] and various DNAzyme-based systems [18]. Perhaps one of the most versatile DNA amplifiers is the catalytic hairpin assembly (CHA), originally developed by Pierce and coworkers [5].…”

Section: Introductionmentioning

confidence: 99%

l-DNA-Based Catalytic Hairpin Assembly Circuit

Kabza

Sczepanski

2020

Molecules

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Isothermal, enzyme-free amplification methods based on DNA strand-displacement reactions show great promise for applications in biosensing and disease diagnostics but operating such systems within biological environments remains extremely challenging due to the susceptibility of DNA to nuclease degradation. Here, we report a catalytic hairpin assembly (CHA) circuit constructed from nuclease-resistant l-DNA that is capable of unimpeded signal amplification in the presence of 10% fetal bovine serum (FBS). The superior biostability of the l-DNA CHA circuit relative to its native d-DNA counterpart was clearly demonstrated through a direct comparison of the two systems (d versus l) under various conditions. Importantly, we show that the l-CHA circuit can be sequence-specifically interfaced with an endogenous d-nucleic acid biomarker via an achiral peptide nucleic acid (PNA) intermediary, enabling catalytic detection of the target in FBS. Overall, this work establishes a blueprint for the detection of low-abundance nucleic acids in harsh biological environments and provides further impetus for the construction of DNA nanotechnology using l-oligonucleotides.

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“…[20][21][22][23] The peroxidase activity is strongly dependent on the specific G4 structures and has been widely employed as a signal amplification tool for detection of nucleic acids, protein, metal ions, and small molecules. [23][24][25][26][27][28] However, the used oxidant H 2 O 2 is concentration decisive for the peroxidase activity [20] and its intrinsic instability is detrimental for reproducibility of the DNAzyme activity-based devices. Additionally, another additive must be further needed to temporally stop the catalytic reaction at the desired incubation time.…”

Section: Introductionmentioning

confidence: 99%

G‐Quadruplex‐Based Photooxidase Driven by Visible Light

Gao

Tong

et al. 2019

ChemCatChem

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The G‐quadruplex (G4)/hemin entity has been widely used as a peroxidase‐mimic DNAzyme to catalyze the substrate oxidation with exogenous and concentrated H2O2 as oxidant for developing various devices. Herein, a G4‐based oxidase‐mimic DNAzyme that can be driven by visible light was developed. The oxidant is in situ produced by light irradiation. As a natural photosensitizer, Hypericin (Hyp) alone in solution is inactive because of aggregation. However, the binding with G4 triggers the fluorescence emission and activates Hyp to produce singlet oxygen (1O2) by energy transfer to the dissolved oxygen. Therefore, the G4/Hyp entity can serve as a photooxidase via the 1O2 pathway to catalyze the substrate oxidation. Since the G4‐bound Hyp can be excited by almost the whole range of visible light, the photooxidase should cover a wide range of photocatalytic applications. Similar to the peroxidase‐mimic DNAzyme, the G4 sequence can regulate the photooxidase activity and metal ions can serve as efficient cofactors to activate the photooxidase capacity for an inactive G4 structure. This work provides an alternative to build a versatile G4‐based photooxidase with straightforward tunability of its activity.

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DNAzyme-Mediated Assays for Amplified Detection of Nucleic Acids and Proteins

Cited by 194 publications

References 208 publications

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

l-DNA-Based Catalytic Hairpin Assembly Circuit

G‐Quadruplex‐Based Photooxidase Driven by Visible Light

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