A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice

Ferdinand Greiss (), Nicolas Lardon, Leonie Schütz, Yoav Barak, Shirley S. Daube, Elmar Weinhold, Vincent Noireaux and Roy Bar-Ziv ()
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Ferdinand Greiss: Weizmann Institute of Science
Nicolas Lardon: Max Planck Institute for Medical Research
Leonie Schütz: RWTH Aachen University
Yoav Barak: Weizmann Institute of Science
Shirley S. Daube: Weizmann Institute of Science
Elmar Weinhold: RWTH Aachen University
Vincent Noireaux: University of Minnesota
Roy Bar-Ziv: Weizmann Institute of Science

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.

Date: 2024
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DOI: 10.1038/s41467-024-45186-2

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