RNA aptamers: promising tools in synthetic biology

Daniel Kelvin; Beatrix Suess

doi:10.1515/auto-2024-0002

Article

RNA aptamers: promising tools in synthetic biology

Daniel Kelvin
Daniel Kelvin received his master’s degree in technical biology from the Technical University of Darmstadt, Germany, in 2021. He is currently employed as a PhD candidate in the Suess group at the biological department of the TU Darmstadt. His current research interests include rational and computational (machine learning) design strategies for the optimization of RNA-based genetic regulatory elements (riboswitches) with logic gate switching patterns.
and Beatrix Suess
Beatrix Suess studied biology in Greifswald and Darmstadt and received her PhD from the Friedrich Alexander University in Erlangen-Nürnberg in 1998 and continued her research as an independent group leader. She was a visiting researcher with Ron Breaker at Yale University. In 2007, she was appointed Associate Professor for Chemical Biology at Goethe-University in Frankfurt. In 2012, she joined TU Darmstadt where she is a founding member of the Centre for Synthetic Biology. Her research interest is synthetic RNA biology.

Published/Copyright: June 28, 2024

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From the journal at - Automatisierungstechnik Volume 72 Issue 7

Abstract

Synthetic elements made entirely of RNA are suitable as regulatory elements in genetically modified systems and as biosensors. Such RNA aptamers are highly structured nucleotide sequences capable of specifically binding a target molecule. De novo selection of aptamers against a wide variety of potential targets is possible. By integrating RNA aptamers as binding domains into natural or synthetically designed regulatory circuits in the form of so-called riboswitches, new regulatory mechanisms can be generated that do not require additional regulatory elements. In addition, these binding domains can be used in cell-free systems to perform highly specific and affine molecular detection assays. By presenting two well-established aptamer designs, we aim to demonstrate the potential of RNA aptamer-based riboswitches and biosensors in various applications.

Zusammenfassung

Synthetische Elemente, die vollständig aus RNA bestehen, eignen sich als regulatorische Einheiten in gentechnisch veränderten Systemen und als Biosensoren. Solche RNA-Aptamere sind hochstrukturierte Nukleotidsequenzen, die mit hoher Spezifität an ein Zielmolekül binden. Es gibt RNA-Aptamere gegen eine Vielzahl an Molekülen, da diese durch eine de novo Selektion ausgehend von einer großen Anzahl zufälliger RNA-Sequenzen selektiert werden können. Durch Integration solcher Aptamere als Bindungsdomänen in Form sogenannter Riboswitches (RNA-Schalter) in natürliche oder synthetisch genetische Schaltkreise können neue Regulationsmechanismen erzeugt werden, die ohne zusätzliche Regulationselemente auskommen. Darüber hinaus können diese Bindungsdomänen in zellfreien Systemen verwendet werden, um hochspezifische und affine molekulare Zielnachweisverfahren durchzuführen. Wir zeigen das Potenzial von RNA-Aptameren in Form von Riboswitches und Biosensoren für verschiedene Anwendungen auf.

Keywords: aptamer; riboswitch; synthetic biology; tetracycline

Schlagwörter: Aptamer; Riboswitch; Synthetische Biologie; Tetracyclin

Corresponding author: Beatrix Suess, Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany; and Centre for Synthetic Biology, TU Darmstadt, 64287 Darmstadt, Germany, E-mail: bsuess@bio.tu-darmstadt.de

About the authors

Daniel Kelvin

Daniel Kelvin received his master’s degree in technical biology from the Technical University of Darmstadt, Germany, in 2021. He is currently employed as a PhD candidate in the Suess group at the biological department of the TU Darmstadt. His current research interests include rational and computational (machine learning) design strategies for the optimization of RNA-based genetic regulatory elements (riboswitches) with logic gate switching patterns.

Beatrix Suess

Beatrix Suess studied biology in Greifswald and Darmstadt and received her PhD from the Friedrich Alexander University in Erlangen-Nürnberg in 1998 and continued her research as an independent group leader. She was a visiting researcher with Ron Breaker at Yale University. In 2007, she was appointed Associate Professor for Chemical Biology at Goethe-University in Frankfurt. In 2012, she joined TU Darmstadt where she is a founding member of the Centre for Synthetic Biology. Her research interest is synthetic RNA biology.

Acknowledgments

The work was supported by the Deutsche Forschungsgemeinschaft (SFB902/A2) and ONR Global #N62909-20-1-2035.

Research ethics: Not applicable.
Author contributions: The authors have accepted responsibility for the entire content of this manuscript and approved its submission.
Competing interests: The authors state no conflict of interest.
Research funding: The work was supported by the Deutsche Forschungsgemeinschaft.
Data availability: Not applicable.

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Received: 2023-12-29

Accepted: 2024-05-13

Published Online: 2024-06-28

Published in Print: 2024-07-26

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Keywords for this article

aptamer; riboswitch; synthetic biology; tetracycline