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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RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs
E. J. Strobel, K. E. Watters, D. Loughrey, J. B. Lucks. Current Opinion in Biotechnology. (2016). doi: 10.1016/j.copbio.2016.03.019
Links: Journal, PDF, Blog PostAbout
A review of current discoveries in RNA biology, including an overview of high throughput experimental methods for uncovering RNA structures.
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Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators
M. K. Takahashi, K. E. Watters, P. M. Gaspar, T. R. Abbott, P. D. Carlson, A. A. Chen, J. B. Lucks. RNA. (2016). doi: 10.1261/rna.054916.115
Links: Journal, PDF, SHAPE-Seq DataSets: RMDB Entries, Blog PostAbout
Here we use SHAPE-Seq to interrogate a series of engineered RNA transcriptional attentuators to find reactivity signatures that correlate with function. We then use these principles to design new attenuators that can function in cells. Molecular dynamics simulations are used to reveal a critical need for hairpin stem flexibility for transcriptional attenuator function.
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Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq
K. E. Watters, Timothy R. Abbott, J. B. Lucks. Nucleic Acids Research. (2015). doi: 10.1093/nar/gkv879
Links: Journal, PDF, SHAPE-Seq DataSets: RMDB Entries, Blog PostAbout
In this paper, a method is developed to characterize RNA structure and function simultaneously with SHAPE-seq and functional assays. This approach is then applied to correlate RNA structure with function of synthetic RNA-RNA regulatory pairs and endogenous RNAs in E. coli.
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Engineered Protein Machines: Emergent Tools for Synthetic Biology
C. J. Glasscock, J. B. Lucks, M. P. DeLisa. Cell Chemical Biology. (2016). doi: 10.1016/j.chembiol.2015.12.004
Links: Journal, PDF, Blog PostAbout
This review article highlights the progress made in understanding, engineering and repurposing bacterial protein machines for use in synthetic biology. In particular, it discusses efforts in engineering DNA/RNA replication and synthesis machinery, orthogonal ribosomes, as well as protein folding and translocation machinery. The article ends with applications of these synthetic machineries in biotechnology such as the development of new therapeutics and vaccines.
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Characterizing and prototyping genetic networks with cell-free transcription-translation reactions
M. K. Takahashi#, C. A. Hayes#, J. Chappell, Z. Z. Sun, R. M. Murray, V. Nouireaux*, J. B. Lucks*. Methods. (2015). doi: 10.1016/j.ymeth.2015.05.020 # = Equal contribution
Links: Jounral, PDF, BioRxiv (Open Access)About
This paper, born out of a Cold Spring Harbor laboratory course, describes how to use cell-free transcription-translation systems to rapidly build and test RNA-regulated genetic circuits, including descriptions of simple experiments, important controls, and how to interpret the data.