Uncovering the principles of molecular design for biology, medicine and biotechnology
Our research
We are a group of energetic scientists driven to understand and improve our relationship with the natural world. Our molecule of interest, RNA, is similar to DNA, but is more versatile within the cell. We study how the structure of RNA plays a role in its cellular jobs, how cells use molecules like RNA to monitor and respond to their changing environments, and how we can use these molecules in cell-free systems to monitor our own environments for health and sustainability.
News
Northwestern University scientists sprint to develop new kind of rapid coronavirus test, Chicago Tribune
Simple test could prevent fluoride-related disease, Science Daily
Recent Publications
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Teaching systematic, reproducible model development using synthetic biology
K. E. Dray, K. S. Dreyer, J. B. Lucks, J. N. Leonard. Chemical Engineering Education (2023). doi: 10.18260/2-1-370.660-132665
Links: Journal , PDFAbout
We present an educational unit to teach computational modeling, through the lens of synthetic biology. Lectures, code, and homework questions provide conceptual and practical introductions to each computational method involved in the model development process, along with perspectives on how methods can be iterated upon.
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A transient intermediate RNA structure underlies the regulatory function of the E. coli thiB TPP translational riboswitch
K. E. Berman, R. Steans, L. M. Hertz, J. B. Lucks. RNA (2024). doi: 10.1261/rna.079427.122
Links: Journal, PDF, BioRxivAbout
This paper we investigate the role of cotranscriptional RNA strand displacement on the E. coli thiB TPP riboswitch. Previous work has demonstrated the importance of strand displacement in the switching mechanism of transcriptional riboswitches, but here we apply this hypothesis to a translational riboswitch using cellular fluorescence assays. Our results suggest that an intermediate structure can strand displace the P1 helix allowing the riboswitch to switch between ribosome binding site sequestering and anti-sequestering stem.
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Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo
D. Z. Bushhouse, J. B. Lucks. Nucleic Acids Research (2023). doi: 10.1093/nar/gkad110
Links: Journal, PDF, BioRxivAbout
We investigated how internal strand displacement controls transcriptional riboswitch function using the C. beijerinckii ZTP riboswitch as a model. By combining mutagenesis and E. coli expression assays, we showed that slowing strand displacement can precisely tune riboswitch dynamic range and even invert regulatory logic, revealing how this mechanism shapes natural riboswitch function and providing a strategy to optimize synthetic riboswitches for biotechnology.
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The accuracy and usability of point-of-use fluoride biosensors in rural Kenya
W. Thavarajah, P. M. Owuor, D. R. Awuor, K. Kiprotich, R. Aggarwal, J. B. Lucks, S. L. Young. NPJ Clean Water (2023). doi: 10.1038/s41545-023-00221-5
Links: Journal, PDFAbout
Here we evaluated a point-of-use fluoride biosensor in Nakuru County, Kenya, assessing both accuracy and usability with local residents. The biosensor accurately identified elevated fluoride in nearly 90% of samples, and participants were able to use and interpret the tests with minimal difficulty, demonstrating the potential for scalable, accessible water quality monitoring to support safe drinking water worldwide.
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Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles
M. A. Boyd, W. Thavarajah, J. B. Lucks, N. P. Kamat. Science Advances (2023). doi: 10.1126/sciadv.add6605
Links: Journal, PDF, BioRxivAbout
This study demonstrates robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing for the detection of fluoride. By tuning membrane composition, we achieved robust, protected, and environmentally relevant sensing, demonstrating that encapsulated artificial cell platforms can provide controllable, genetically encoded detection of small molecules in real-world samples.