DNA-Based Enzyme Reactors and Systems
Abstract
:1. Introduction
2. Building with DNA Molecules and Enzymes
2.1. DNA Nanostructures
2.2. DNA-Enzyme Conjugates and Arrays
3. Enzyme Reactors and Cascades
4. Enzymatic Nanodevices with Motion
4.1. Mechanical Regulatory DNA-Enzyme Devices
4.2. Autonomous Molecular Systems
5. Enzyme Containers and Carriers
5.1. DNA Containers for Enzymes
5.2. Cellular Delivery of DNA-Enzyme Conjugates
6. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
2D | Two-dimensional |
3D | Three-dimensional |
β-gal | β-galactosidase |
ABTS | 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) |
AFM | Atomic force microscopy |
B-DNA | Double-helical DNA in B-form (geometry attribute) |
BSA | Bovine serum albumin |
DNA | Deoxyribonucleic acid |
dsDNA | double-stranded DNA |
DX | Double-crossover |
eGFP | Enhanced green fluorescent protein |
FRET | Förster resonance energy Transfer |
G6pDH | Glucose-6-phosphate dehydrogenase |
GOx | Glucose oxidase |
HRP | Horseradish peroxidase |
LDH | Lactate dehydrogenase |
LUC | Lucia luciferase |
MDH | Malate dehydrogenase |
NAD+ | Nicotinamide adenine dinucleotide (oxidized) |
NADH | Nicotinamide adenine dinucleotide (reduced) |
nt | nucleotide |
NTV | NeutrAvidin |
OAA | Oxaloacetate |
OAD | Oxaloacetate decarboxylase |
PDMAEMA | Poly(dimethylaminoethyl methacrylate) |
PEG | Polyethylene glycol |
PMS | Phenazine methosulfate |
RNA | Ribonucleic acid |
ssDNA | Single-stranded DNA |
TMB | 3,3′,5,5′-tetramethylbenzidine |
XDR | Xylitol dehydrogenase |
XR | Xylose reductase |
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Type | Function | Key Aspects |
---|---|---|
A glucose oxidase (GOx) – horseradish peroxidase (HRP) cascade on a DNA origami [43]. | The enzyme positions on the DNA origami template can be tuned. | The cascade activity is highly dependent on the spacing between the enzymes; the highest activity was found at a 10 nm distance. |
A GOx-HRP cascade on a DNA origami that can be rolled into tubular shape [44]. | The idea is similar to the above, but here the semi-confined tubular geometry could enable shielding. | The enzymes in the semi-confined geometry show higher enzymatic activity than the free enzyme controls. |
A swinging arm between malate dehydrogenase (MDH) and glucose-6-phosphate dehydrogenase (G6pDH) assembled on a double-crossover (DX) DNA tile [45]. | The DNA strand acts as a flexible arm that channels the cofactor transfer between the hydrogenases in the complex. | The enzyme activity achieved by the swinging arm is significantly higher than in the case of freely diffusing cofactor. |
A tubular DNA origami nanoreactor with GOx-HRP pairs [46]. | The nanoreactor is comprised of two units: GOx- and HRP-loaded DNA origamis that can be combined into a complete cascade reactor. | Single origami units and the complete reactor equipped with binding sites show higher activity than the controls without binding sites. |
A xylose reductase (XR) – xylitol dehydrogenase (XDR) cascade on a DNA origami [47]. | The enzymes are attached to origami via DNA-binding protein adaptors resulting in an artificial enzyme cascade. | The efficiency of the cascade reaction is more dependent on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes. |
A three-enzyme pathway assembled by a DNA nanostructure [48]. | MDH, oxaloacetate decarboxylase (OAD) and lactate dehydrogenase (LDH) are organized at the corners of the triangular DNA nanostructure, thus forming a three-enzyme cascade. | Activity of the cascade depends more on the geometric patterns of enzymes than the interenzyme spacings. |
Type | Function | Key Aspects |
---|---|---|
DNA nanotweezers [49,50,51,52] equipped with cascade pairs or with the enzyme and its cofactor. | The tweezers can be opened and closed through a strand-displacement reaction. | The enzyme activity can be controlled by switching the tweezers reversibly. |
A tubular DNA origami nanoreactor [53]. | The lid of the tube can be opened and closed with the help of lock and key strands. | Flowthrough of the compounds into the confined reaction chamber is controlled by the lid. |
A four-arm DNA origami nanoactuator [54]. | A distance change in a driver site can be propagated to the mirror site containing binding sites for cargo molecules. | The actuator can be driven using different mechanisms, and it can be used for, e.g., tuning fluorescence behavior of enhanced fluorescent protein (eGFP). |
Aptamer-based logical circuit [55]. | The autonomous logical circuit controls α-thrombin activity through the convertor, controller and generator modules. | α-thrombin aids blood coagulation, and therefore systems such as this may find intriguing biomedical uses. |
Type | Function | Key Aspects |
---|---|---|
Hollow DNA origami containers [56,57,58]. | These structures could be used in encapsulating molecular cargo. | Examples include successful opening and closing mechanisms for conceivable drug release. |
DNA origami half-cages [59] that can be arranged into a closed box. | The closed geometry shields the enzymatic reactions (such as the glucose oxidase (GOx) – horseradish peroxidase (HRP) cascade) against proteases. | Activity of a single enzyme can be enhanced by encapsulating it into the box. |
A tubular DNA origami nanocarrier [60]. | The carrier acts as a host for luciferase enzymes. | Luminescence of the cargo can be modulated by coating the carrier with cationic polymers. |
A box-like DNA origami container [61]. | The box facilitates the binding of proteins (such as bovine serum albumin (BSA)) in the cavity of the origami. | Bound proteins can be released by light. |
A switchable DNA cage [62]. | The cage can trap and release HRP through a conformational change. | The conformational change can be controlled by temperature. |
A β-galactosidase (β-gal) protein coated by DNA strands [63]. | DNA-coating significantly increases cellular delivery of the enzymes. | The approach is highly modular, and importantly, the enzymes retain their activity in the transfection. |
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Linko, V.; Nummelin, S.; Aarnos, L.; Tapio, K.; Toppari, J.J.; Kostiainen, M.A. DNA-Based Enzyme Reactors and Systems. Nanomaterials 2016, 6, 139. https://doi.org/10.3390/nano6080139
Linko V, Nummelin S, Aarnos L, Tapio K, Toppari JJ, Kostiainen MA. DNA-Based Enzyme Reactors and Systems. Nanomaterials. 2016; 6(8):139. https://doi.org/10.3390/nano6080139
Chicago/Turabian StyleLinko, Veikko, Sami Nummelin, Laura Aarnos, Kosti Tapio, J. Jussi Toppari, and Mauri A. Kostiainen. 2016. "DNA-Based Enzyme Reactors and Systems" Nanomaterials 6, no. 8: 139. https://doi.org/10.3390/nano6080139
APA StyleLinko, V., Nummelin, S., Aarnos, L., Tapio, K., Toppari, J. J., & Kostiainen, M. A. (2016). DNA-Based Enzyme Reactors and Systems. Nanomaterials, 6(8), 139. https://doi.org/10.3390/nano6080139