Regulation of an Enzyme Cascade Reaction by a DNA Machine

Xin, Ling; Zhou, Chao; Yang, Zhongqiang; Li, Dongsheng

doi:10.1002/smll.201300019

Cited by 148 publications

(151 citation statements)

References 50 publications

(11 reference statements)

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“…The increase in reaction velocity of HRP causes a change in the product formation curve (Fig. 2b), which resembles the changes observed when GOx and HRP are placed on DNA scaffolds91017.…”

Section: Resultssupporting

confidence: 61%

“…Ultimately, the overall activity will be limited by the maximal reaction rate of the slower enzyme1320. Proximity in itself should not influence the maximal reaction rate of either enzyme; however, the reported activity enhancements appear to persist over the entire observation time which would indicate that the limiting maximal reaction rate has increased111721. This contradiction between the theoretical analysis and experimental observations has not yet been resolved.…”

mentioning

confidence: 94%

“…co-assembled the GOx–HRP pair on DNA origami and observed 15 times higher activity when the distance between two enzymes is 10 nm. In contrast, Xin et al 17. placed the GOx and HRP even closer using a similar strategy but found only a 1.5-fold activity enhancement.…”

mentioning

confidence: 96%

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Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

2016

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A proximity effect has been invoked to explain the enhanced activity of enzyme cascades on DNA scaffolds. Using the cascade reaction carried out by glucose oxidase and horseradish peroxidase as a model system, here we study the kinetics of the cascade reaction when the enzymes are free in solution, when they are conjugated to each other and when a competing enzyme is present. No proximity effect is found, which is in agreement with models predicting that the rapidly diffusing hydrogen peroxide intermediate is well mixed. We suggest that the reason for the activity enhancement of enzymes localized by DNA scaffolds is that the pH near the surface of the negatively charged DNA nanostructures is lower than that in the bulk solution, creating a more optimal pH environment for the anchored enzymes. Our findings challenge the notion of a proximity effect and provide new insights into the role of DNA scaffolds.

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“…The increase in reaction velocity of HRP causes a change in the product formation curve (Fig. 2b), which resembles the changes observed when GOx and HRP are placed on DNA scaffolds91017.…”

Section: Resultssupporting

confidence: 61%

mentioning

confidence: 94%

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Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

2016

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“…Following the use of DNA tweezers to regulate protein binding, a similar design has been used to attach two enzymes of GOx and HRP to both arm ends of DNA tweezers. 72 As this reaction occurs, the diffusion distance of intermediate H 2 O 2 determines the rate of this enzymatic cascade reaction. By deliberately tuning the state of DNA tweezers in closed and open states, the distance between GOx and HRP can be adjusted from several nanometers to~18 nm.…”

Section: Dynamic Regulation Of Nps With Dnamentioning

confidence: 99%

Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology

Yang

Liu

2015

NPG Asia Mater

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Nanoparticles are among the most fascinating materials because of their unique size-dependent properties. The spatial positioning of the nanoparticles with a nanoscale precision will greatly enhance their potential for use in the fabrication of functional materials and devices. Recently, the development of DNA nanotechnology has enabled the construction of two-and three-dimensional, precisely addressable nanostructures and devices based on DNA sequence design and programmable assembly. Advances in conjugating DNA with nanoparticles can bridge these two technologies and provide scientists with a new tool to study material transportation and energy transfer at a nanometer scale. In this review, we summarize the recent progress in this emerging research field, which includes not only the static arrangements of inorganic nanoparticles but also the dynamic regulation of organic and biological units at a nanometer scale. With the rapid development in this field, new challenges and new possibilities will emerge and bring about fruitful achievements with a significant impact on future work.

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“…28,29 Among these nanodevices, DNA tweezers have gained much attention for applications in cascade reaction and interaction research 8, 30 since the first report in 2000. 6 The molecular tweezer can be regulated by target for fluorescent detection.…”

Section: ■ ■ ■ ■ Introduction Sectionmentioning

confidence: 99%

Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs

Cheng

et al. 2016

Anal. Chem.

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A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system. The binary target inputs can be used for successful building of AND logic gate, which is validated by polyacrylamide gel electrophoresis, surface plasmon resonance and the biosensing signal. The developed biosensing system shows a linear response of the output chemiluminescence signal to input binary miRNAs with a detection limit of 30 fM. It can be used for miRNAs analysis in complex sample matrix. This system provides a simple and reusable platform for logic gate operation and enzyme-free, highly sensitive, and specific multianalysis of miRNAs.

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Regulation of an Enzyme Cascade Reaction by a DNA Machine

Cited by 148 publications

References 50 publications

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade

Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology

Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs

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