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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

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Programming Dissipation Systems by DNA Timer for Temporally Regulating Enzyme Catalysis and Nanostructure Assembly.

Zhaohui Qin¹, Yu Liu¹, Linghao Zhang¹

¹College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.

|September 14, 2022

Summary

This study introduces a DNA-based artificial system that uses a molecular timer to precisely control energy dissipation. This programmable timer regulates complex processes like catalysis and nanostructure assembly, enabling intelligent artificial reaction networks.

Keywords:

DNA nanostructure assembly Dissipative DNA nanotechnology Enzyme catalysis Molecular timer λ-Exonuclease

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Area of Science:

Biochemistry
Nanotechnology
Systems Chemistry

Background:

Living cells utilize precise temporal control in energy-dissipating processes like catalysis and assembly.
Artificial systems often lack sophisticated temporal regulation found in biological systems.

Purpose of the Study:

To develop a DNA-based artificial dissipative nonequilibrium system with a built-in molecular timer.
To demonstrate programmable control over the lifetime of transient states in artificial systems.

Main Methods:

Utilized lambda-exonuclease (λ Exo) for processive DNA digestion, acting as an orthogonal molecular timer.
Integrated the DNA timer with enzyme catalysis and DNA nanotube (DNT) assembly networks.
Engineered dynamic activation of catalysis and dynamic disassembly of DNTs.

Main Results:

Achieved programmable regulation of transient-state lifetimes using the DNA timer.
Demonstrated dynamic activation of enzyme catalysis controlled by the molecular timer.
Showcased dynamic disassembly of DNA nanotubes (DNTs) with timer-encoded lifetimes.

Conclusions:

Developed nontrivial dissipative systems with integrated molecular timers.
The DNA timer enables accurate encoding of state lifetimes in artificial networks.
This approach provides a tool for creating complex and intelligent artificial reaction networks and nanostructures.