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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Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements
K. E. Watters, K. Choudhary, S. Aviran, J. B. Lucks, K. L. Perry, J. R. Thompson. Nucleic Acids Research. (2017). doi: 10.1093/nar/gkx1273
Links: Jounral, PDF, SHAPE-Seq DataSets: RMDB EntriesAbout
Our report on the SHAPE-Seq-determined structure of the cucumber mosaic virus and how RNA structural elements are selected for for viral infectivity.
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Turning it up to 11: Modular proteins amplify RNA sensors for sophisticated circuitry
J. Chappell, J. B. Lucks. Cell Systems. (2016). doi: 10.1016/j.cels.2016.12.004
Links: Journal, PDF, Blog PostAbout
Our perspective on Wang et al. “Design and construction of generalizable RNA-protein hybrid controllers by level-matched genetic signal amplification” in Cell Systems. We describe how important it is to match transfer curves for correct genetic circuit function.
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Cotranscriptional folding of a riboswitch at nucleotide resolution
K. E. Watters#, E. J. Strobel#, A. M. Yu, J. T. Lis, J. B. Lucks. Nature Structure and Molecular Biology. (2016). doi: 10.1038/nsmb.3316 # = Equal contribution
Links: Journal, PDF,About
This work demonstrates a novel approach of combining our previous SHAPE-seq RNA structure probing method with in vitro transcriptional roadblocks to observe how RNA folds during transcription. Using this method, we observed intermediate structural states of the signal recognition particle RNA and the fluoride riboswitch.
SHAPE-Seq DataSets: RMDB Entries
Sequencing Reads: SRA Entries
Blog Posts:
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Mapping RNA structure in vitro with SHAPE chemistry and next-generation sequencing (SHAPE-Seq)
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Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
K. E. Watters, A. M. Yu, E. J. Strobel, A. H. Settle, J. B. Lucks. Methods. (2016). doi: 10.1016/j.ymeth.2016.04.002
Links: Journal, PDF, BioRxiv (Open Access), SHAPE-seq DataSets: RMDB Entries, Blog PostAbout
This methods paper provides the details to understand and perform SHAPE-seq v2.1 in cells and in vitro. Two key improvement over v2.0 are increased flexibility in barcoding the cDNA library for sequencing and a selective PCR step in library preparation to reduce unwanted side products.