RNA Synthetic Biology

RNA is a ubiquitous molecule of life that plays intimate roles in how cells function and make decisions. These same properties can be harnessed to create a new generation of engineering tools to further interrogate the properties of biology and control how cells behave. The RNA synthetic biology group aims to better understand the roles RNA plays in biology and to exploit these roles to improve how we study, diagnose, and treat infectious diseases in humans. This group is located at the Helmholtz Institute for RNA-based Infection Research (HIRI).


selected publications

Liao C, Ttofali F, Slotkowski RA, Denny SR, Cecil TD, Leenay RT, Keung AJ, Beisel CL.
Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis.
Nat Commun 2019, 10(1):2948

Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V
Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System
Mol Cell 2018, 69(1): 146-157

Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
Mol Cell 2016, 62(1): 137-147

Luo ML, Mullis AS, Leenay RT1, Beisel CL
Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression
Nucleic Acids Res 2015, 43(1): 674-681

Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL
Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems
MBio 2014, 5(1): e00928-13

Recent publications

Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA.
Targeted transcriptional modulation with Type I CRISPR-Cas systems in mammalian cells.
Nat Biotechnol (in press)

Wandera KG, Collins SP, Wimmer F, Marshall R, Noireaux V, Beisel CL. (2019)
An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system.
Methods (in press)

Jacobsen T, Liao C, Beisel CL. (2019)
The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs.
FEMS Microbiol Letters 366(8):fnz085.

Garenne D, Beisel CL, Noireaux V. (2019)
Characterization of the all-E. coli transcription-translation system myTXTL by mass spectrometry.
Rapid Commun Mass Spec 33(11):1036-1048.

Liao C, Slotkowski RA, Achmedov T, Beisel CL. (2019)
The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays.
RNA Biol 16(4):404-412.

Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. (2019)
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator.
Biotechnol Bioeng 116(5):1139-1151.

Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL. (2019)
Genome editing with CRISPR-Cas9 in Lactobacillus plantarum revealed that editing outcomes can vary across strains and between methods.
J Biotechnol 14(3):e1700583.

Collias D, Marshall R, Collins SP, Beisel CL, Noireaux V. (2019)
An educational module to explore CRISPR technologies with a cell-free transcription-translation system.
Synth Biol 4(1):ysz005.

Martino ME, Joncour P, Leenay R, Gervais H, Shah M, Hughes S, Gillet B, Beisel C, Leulier F. (2018)
Bacterial adaptation to host diet is a key evolutionary force shaping host-microbe symbiosis.
Cell Host Microbe 24(1):109-119.

Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9
Mol Cell 2018, 69(5): 893-905

Further Information

A current overview of the team and further information about the research group can be found on the HIRI page.


  • Novel COVID testing method

    CRISPR discovery from Würzburg paves the way for LEOPARD

    Am I infected with SARS-CoV-2? Is it one of the dangerous variants? Being able to answer these and more questions with a single efficient diagnostic test can be decisive for gauging the spread of disease and selecting the right therapy. In a study published today in the journal "Science", researchers from Würzburg at the Helmholtz Institute for RNA-based Infection Research (HIRI), a site of the Helmholtz Centre for Infection Research (HZI) in cooperation with the Julius Maximilians University (JMU), tackle this challenge with a new CRISPR discovery they translated into a diagnostic platform called LEOPARD.

  • 1 cure for ALL viruses? 6 new research teams in the challenge by the Federal Agency for Disruptive Innovations [Video in German]

    Six research teams have entered the second phase of the SPRIND Challenge "A Quantum Leap for New Antiviral Agents" with their approach to developing new antiviral agents. Scientists from the Helmholtz Centre for Infection Research are involved in three of the funded projects. YouTuber Jacob Beautemps introduces the teams.

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