A modular DNA origami-based enzyme cascade nanoreactor

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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“…Linko et al 32. encapsulated GOx and HRP in DNA origami tubes with dimensions of 33 × 27 × 60 nm 3 .…”

Section: Resultsmentioning

confidence: 99%

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

2016

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“…Fu et al [58] fabricated multienzyme cascades on DNA templates, where substrate channeling was realized using a DNA strand as a flexible swinging arm between the immobilized enzymes. Linko et al [59] showed how modular DNA origami building blocks could be assembled together to form a tubular enzyme cascade nanoreactor ( Figure 2C) for detecting glucose. The device could find use as a biosensor or a delivery vehicle for enzymatic payloads e.g.…”

Section: Smart Dna Nanodevices and Molecular Platformsmentioning

confidence: 99%

“…(B) A switchable tweezer-like enzymatic nanoreactor [57]. (C) A tubular DNA origami-based enzyme cascade nanoreactor for biosensing [59]. (D) A cargo mimic for dynein motor proteins [60].…”

Section: Shape-complementarity-based Constructionmentioning

confidence: 99%

DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices

Linko

Ora

Kostiainen

2015

Trends in Biotechnology

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228

166

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Emerging DNA nanotechnologyThe field of structural DNA nanotechnology started around 30 years ago when Ned Seeman performed pioneering research with DNA junctions and lattices [1]. To date, a cornucopia of different DNA nanostructures and shapes based on WatsonCrick basepairing [2] have been designed and demonstrated, and the whole research area has enjoyed a rapid progress especially during the past decade [3]. The key player in the fast development of DNA nanotechnology has been the invention of DNA origami in 2006 [4]. The DNA origami method is based on folding a long single-stranded "DNA scaffold strand" into a customized shape with a set of short synthetic staple strands. The robustness of the technique has made it widely accessible.Since then, the method has been generalized to 3D-fabrication [5][6][7][8][9][10], and it enables shapes with custom curvatures, twists and bends [11,12]. Very recently, techniques for modular scaffold-free fabrication [13,14], 3D meshing and wireframe-based approaches [15][16][17], as well as shape-complementarity-based construction [18] of DNA objects have been introduced. In addition, powerful computational tools for designing and analyzing DNA nanostructures have been developed [19][20][21], which appreciably help researchers to create their own DNA nanoarchitectures for any conceivable application. Table 1 lists and 2 describes the novel design strategies that can be used for fabricating diverse DNA origami nanostructures and other complex DNA-based shapes for various nanotechnological purposes.The platonic DNA nanostructures and DNA origamis are by all means remarkably impressive examples of precise engineering and constructing at the nanoscale. However, the attractiveness of the origami method lies in the fact that one can add any desired functionality to the tailored DNA shapes by assembling other biomolecules and molecular components to them with nanometer precision. Importantly, DNA is inherently biocompatible, and its stability can be further tuned by the optional functionalization [20,[22][23][24]. Aforementioned superior features can be eventually exploited in designing artificial DNA-based biomachinery, such as nucleic acid devices [25] and protein-DNA hybrid structures [26] for nanomedicine and biosensing. In this focused review, we discuss the recent progress of the nanomedical applications of self-assembled DNA systems; especially the drug delivery vehicles and nanomachines based on the DNA origami technique. Towards DNA-based drug delivery vehicles and advanced therapeuticsThe tremendous self-assembly properties of DNA can be exploited in creating various programmable shapes and larger assemblies for cellular delivery for e.g. cancer and enzyme replacement therapy. The very first DNA origami nano-objects proposed to work as molecular containers for drug delivery applications were single-layer origamis, which were further assembled into 3D shapes -a tetrahedron [5] or hollow cubes [6,7] (Fig. 1A). Since then, cellular uptake for various DNA structures (based o...

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“…Several attractive materials and successful strategies have been proposed leading to the design of an arsenal of multienzyme systems for mimicking the natural metabolic pathways in vitro. Examples are the preparations of hydrogels, 15,22 hourglass shaped nanochannel reactor, 23 mesoporous silica nanoparticles, 18,24 formation of inorganic nanocrystal-protein complexes 25 and self-assembled crystals, 26 microbeads, 27,28 DNA nanostructures, 4,5,11,[29][30][31] polymersomes, 14,32 nanoparticles, 33 nanobers, 13,16,34 graphene, 9,35 and metal-organic frameworks (MOFs). 17,36,37 In contrast to other scaffolds, MOFs, which are formed by the self-assembly of metal ions and organic linkers, feature ultrahigh surface area and porosity, uniform pores with tunable sizes, surfaces with variable chemistries, and structural diversity.…”

Section: Introductionmentioning

confidence: 99%

Magnetic metal–organic frameworks as scaffolds for spatial co-location and positional assembly of multi-enzyme systems enabling enhanced cascade biocatalysis

et al. 2017

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Magnetic multi-enzyme nanosystems have been prepared via co-precipitation of enzymes and metalorganic framework HKUST-1 precursors in the presence of magnetic Fe 3 O 4 nanoparticles. The spatial co-localization of two enzymes was achieved using a layer-by-layer positional assembly strategy.Glucose oxidase (GOx) and horseradish peroxidase (HRP) were used as the model enzymes for cascade biocatalysis. By controlling the spatial positions of enzymes, three bienzyme nanosystems GOx@HRP@HKUST-1@Fe 3 O 4 , GOx-HRP@HKUST-1@Fe 3 O 4 and HRP@GOx@HKUST-1@Fe 3 O 4 were prepared in which GOx and HRP containing layers were in close proximity, either encapsulated in the HKUST-1 inner layer, or immobilized on the HKUST-1 outer shell, or randomly distributed in the two MOF layers. Their properties were characterized by transmission electron microscopy, energydispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, thermal gravimetric analysis, and zeta potential measurements. The highest activity was observed at pH ¼ 6 and a temperature of 20 C. Thanks to the favorable positioning of enzymes, the GOx@HRP@HKUST-

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A modular DNA origami-based enzyme cascade nanoreactor

Cited by 197 publications

References 39 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

DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices

Magnetic metal–organic frameworks as scaffolds for spatial co-location and positional assembly of multi-enzyme systems enabling enhanced cascade biocatalysis

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