A Thermophilic Tetramolecular G‐Quadruplex/Hemin DNAzyme

Guo, Yuehua; Chen, Jielin; Cheng, Ming; Monchaud, David; Zhou, Jun; Ju, Huangxian

doi:10.1002/ange.201708964

Cited by 24 publications

(12 citation statements)

References 48 publications

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“…Catalytic activity of G4/hemin complex can be further enhanced by loop/flanking nucleotides which act as a general acid-base during the initial step of the reaction. 31, 34–36, 93 Our simulations provide solid evidence to support this model: the three-nucleotide propeller loops of 1KF1 and single slipped Gs in t13 and t45 (being positioned equivalently to flanking nucleotides) are flexible enough to form a base/hemin/quartet sandwich (Figures 4B and 5). In this arrangement, the base is close to the hemin iron atom thus being suited to bind H 2 O 2 , stabilizing the transition state of the reaction and increasing its rate.…”

Section: Discussionsupporting

confidence: 56%

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

Stadlbauer

Islam

Otyepka

et al. 2020

Preprint

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Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics simulations to scrutinize the G4/hemin interaction. We found that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. Importantly, the simulations do not support several mechanistic possibilities (i.e., the wobbling guanine and the iron-bound water molecule) but rather suggest tentative mechanisms in which the external G-quartet itself is responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Our simulations show that once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD simulation technique are also briefly discussed.Graphical AbstractHemin can bind to G-quadruplex via loop-assisted delivery. The catalytically active structure does not seem to contain an iron-bound water molecule sandwiched in between hemin and G-quadruplex or wobbling guanine.

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Section: Discussionsupporting

confidence: 56%

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

Stadlbauer

Islam

Otyepka

et al. 2020

Preprint

Self Cite

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“…The peroxidase mimicking catalytic activity of G4 DNAzyme catalyzes the oxidation of 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS 2− ) to produce a colorimetric change from a colorless solution to a visible blue-green product (see Figure 9). DNAzyme systems involving other substrates like luminol, 3,3′,5,5′-tetramethylbenzidine sulfate (TMB), 4-chloro-1-naphthol (4-CN) or scopoletin (Sc), in the presence of hydrogen peroxide (H 2 O 2 ) can also be used to produce colorimetric, electrochemical and fluorescence readouts [46,47,48,49,50,51]. However, colorimetric G4-hemin DNAzyme-based biosensors are utilized in diagnostics for its simplicity, fast analysis, low cost and most notably, the ability to detect target molecules visually.…”

Section: G-quadruplex-based Detection Systemmentioning

confidence: 99%

G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing

et al. 2019

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G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.

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“…Previous studies have shown that the structure of the G-quadruplex has a crucial impact on the catalytic efficiency. For example, the DNAzyme formed by parallel G-quadruplex has a much higher catalytic efficiency than that formed by antiparallel G-quadruplex [ 6 ], and that formed by G-quadruplex with adenosine at the 3′-end shows an enhanced catalytic activity [ 7 ], while that formed with adenosines at both the 3′- and 5′-ends can efficiently catalyze the oxidation even at 95 °C [ 8 ]. Besides, two or more individual G-quadruplexes stacked on top of each other to form a multimeric G-quadruplex have a synergistic enhancement effect on the catalytic activity of the DNAzyme [ 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection

Zhang

et al. 2021

Molecules

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G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H2O2-mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.

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A Thermophilic Tetramolecular G‐Quadruplex/Hemin DNAzyme

Cited by 24 publications

References 48 publications

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing

Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection

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