Controlling biocatalytic cascades with enzyme–DNA dynamic networks

Abstract

Cellular transformations, such as gene expression or temporal protein activities, are controlled by complex stimuli-responsive network circuitries regulated by enzymes, metabolites or transcription factors. Inspired by nature, extensive research efforts are directed to mimic these processes by in vitro chemical systems. Here we report on the assembly of constitutional dynamic networks (CDNs), composed of nucleic acid–enzyme conjugates, that act as modules for triggered, network-driven, biocatalytic cascades and for the intercommunication of network-guided biocatalytic cascades. Two CDNs were assembled—one network includes a constituent module functionalized with glucose oxidase and horseradish peroxidase in spatially close positions, and the second CDN includes a constituent module modified at sterically intimate positions with nicotinamide adenine dinucleotide and alcohol dehydrogenase. Biocatalytic cascades proceed in the two networks and, on the triggered reconfiguration of the CDNs, controlled and switchable biocatalytic cascades in the CDNs are demonstrated. The two CDNs are coupled, and the triggered feedback-driven intercommunication of the networks is realized.

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Fig. 1: Reversible triggered reconfiguration of a network-driven bienzyme cascade.
Fig. 2: Reversible triggered reconfiguration of a network-driven enzyme/cofactor cascade.
Fig. 3: Orthogonal operation of two biocatalytic cascades guided by intercommunicating dynamic networks.
Fig. 4: Feedback-driven intercommunication of networks M and N that activate two coupled biocatalytic cascades.

Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.

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Acknowledgements

Our research is supported by the Israel Science Foundation.

Author information

Affiliations

Authors

Contributions

C.W. performed the experiments, analysed the results and participated in writing the paper. L.Y. participated in the design of CDNs and analysis of the results. I.W. supervised the project.

Corresponding author

Correspondence to Itamar Willner.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Methods, Figs. 1–33, discussion, Tables 1–4, Notes 1–4 and references.

Source data

Source Data Fig. 1

Time-dependent fluorescence changes generated by the DNAzyme reporter units associated with the constituents in CDNs and time-dependent absorbance changes of ABTS∙– in CDNs.

Source Data Fig. 2

Time-dependent fluorescence changes generated by the DNAzyme reporter units associated with the constituents in CDNs and time-dependent absorbance changes induced by ADH/NAD+/MB+ cascade and ADH/NAD+/pyruvic acid cascade.

Source Data Fig. 3

Time-dependent absorbance changes induced by two biocatalytic cascades guided by intercommunicating CDNs.

Source Data Fig. 4

Time-dependent absorbance changes of two biocatalytic cascades guided by feedback-driven intercommunication of coupled CDNs.

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Wang, C., Yue, L. & Willner, I. Controlling biocatalytic cascades with enzyme–DNA dynamic networks. Nat Catal 3, 941–950 (2020). https://doi.org/10.1038/s41929-020-00524-7

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