Tuning the Reactivity of a Substrate for SNAP‐Tag Expands Its Application for Recognition‐Driven DNA‐Protein Conjugation

Zhang, Zhengxiao; Nakata, Eiji; Dinh, Huyen; Saimura, Masayuki; Rajendran, Arivazhagan; Matsuda, Kazunari; Mutoh, T.

doi:10.1002/chem.202103304

Cited by 7 publications

(3 citation statements)

References 63 publications

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“…Upon ligation, the bridged DNA should be a useful platform to assemble not only the pH-sensitive fluorophore as shown in this study, but also other functional molecules introduced on the DNA nanostructures previously [ 31 ]. For example, enzymes of interest can be located on the bridged DNA to encapsulate a defined number of enzymes within a nanoliposome by using the modular adaptors developed by our group [ 32 , 33 , 34 , 35 , 36 , 37 ]. The bridged ring skeleton with spatially assembled enzymes would be converted to a compartment upon the formation of liposome.…”

Section: Discussionmentioning

confidence: 99%

Controlled Assembly of Fluorophores inside a Nanoliposome

Konishi¹,

Nakata²,

Komatsubara³

et al. 2023

Molecules

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Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.

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Section: Discussionmentioning

confidence: 99%

Controlled Assembly of Fluorophores inside a Nanoliposome

Konishi¹,

Nakata²,

Komatsubara³

et al. 2023

Molecules

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“…As reported previously [ 78 ], two enzymes with different pH preferences, xylose reductase (XR) and xylitol dehydrogenase (XDH), were individually assembled on the fully open state of a 3D DNA scaffold through the modular adaptor method [ 79 , 80 , 81 , 82 , 83 , 84 ] in high loading yields. XR was genetically fused to the modular adaptor ZF-SNAP to obtain ZS-XR.…”

Section: Catalytic Enhancement Of Single Type Of Enzyme Assembled On ...mentioning

confidence: 99%

“…In our previous studies, the enzyme cascade reactions derived from D-xylose metabolic pathway were investigated on 2D and 3D DNA scaffolds. The modular adaptor method was applied to stably co-locate enzymes on scaffold with the precise control over enzyme stoichiometry and interenzyme distance [ 79 , 80 , 81 , 82 , 83 , 84 ]. ZS-XR [ 80 ] and G-XDH (adaptor GCN4 fused xylitol dehydrogenase) [ 101 ] were arranged on a three-well DNA scaffold with the alteration of interenzyme distance from 98 nm to 10 nm; it was found that the highest efficiency appeared at a distance of 10 nm, and the intermediates (xylitol and NAD + ) transferred to the downstream enzyme following the Brownian motion ( Figure 12 a) [ 80 ].…”

Section: Enhanced Efficiency Of Enzyme Cascade Reactions On the Dna S...mentioning

confidence: 99%

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

et al. 2022

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Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.

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Dynamic Assembly of Cascade Enzymes by the Shape Transformation of a DNA Scaffold

Lin

Dinh

Morita

et al. 2023

Adv Funct Materials

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Within cells, the close spatial arrangement of cascade enzymes facilitates the channeling of intermediates and enhances cascade reaction efficiency. Reconfigurable DNA nanostructures, owing to their structural controllability and precise spatial addressability, are promising tools for mimicking such processes. In this study, a 3D DNA origami scaffold, with a dynamic shape transformation from its open boat form to a closed hexagonal prism induced by toehold‐mediated strand displacement, is designed to investigate the enzyme cascade reaction of xylose reductase and xylitol dehydrogenase from D‐xylose metabolic pathway. Enzymes are assembled on the DNA scaffold in its open state, which is subsequently closed by the assistance of DNA sequence‐specific closing keys. The enzyme cascade efficiency is much higher in the static encapsulated closed state than in the open state due not only to the enzyme proximity but also the environmental factors of 3D DNA structure. These results provide novel insights into controlling enzyme cascade reactions by inducing the shape transformation of DNA nanostructures and how environmental factors affect the action of multi‐enzyme complexes in the cell.

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Tuning the Reactivity of a Substrate for SNAP‐Tag Expands Its Application for Recognition‐Driven DNA‐Protein Conjugation

Cited by 7 publications

References 63 publications

Controlled Assembly of Fluorophores inside a Nanoliposome

Controlled Assembly of Fluorophores inside a Nanoliposome

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

Dynamic Assembly of Cascade Enzymes by the Shape Transformation of a DNA Scaffold

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