Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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De novo design of a synthetic riboswitch that regulates transcription termination

Manja Wachsmuth, Sven Findeiß, Nadine Weissheimer, Peter F. Stadler and Mario Mörl


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Nucleic Acids Res. 41:2541–2551 (2013)


Riboswitches are regulatory RNA elements typically located in the 50 -untranslated region of certain mRNAs and control gene expression at the level of transcription or translation. These elements consist of a sensor and an adjacent actuator domain. The sensor usually is an aptamer that specifically inter- acts with a ligand. The actuator contains an intrinsic terminator or a ribosomal binding site for transcrip- tional or translational regulation, respectively. Ligand binding leads to structural rearrangements of the riboswitch and to presentation or masking of these regulatory elements. Based on this modular organ- ization, riboswitches are an ideal target for con- structing synthetic regulatory systems for gene expression. Although riboswitches for translational control have been designed successfully, attempts to construct synthetic elements regulating transcrip- tion have failed so far. Here, we present an in silico pipeline for the rational design of synthetic riboswitches that regulate gene expression at the transcriptional level. Using the well-characterized theophylline aptamer as sensor, we designed the actuator part as RNA sequences that can fold into functional intrinsic terminator structures. In the bio- chemical characterization, several of the designed constructs show ligand-dependent control of gene expression in Escherichia coli, demonstrating that it is possible to engineer riboswitches not only for translational but also for transcriptional regulation.


riboswitch design, transcription termination