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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Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems
M. K. Takahashi, J. Chappell, C. A. Hayes, Z. Z. Sun, J. Kim, V. Singhal, K. J. Spring, S. Al-Khabouri, C. P. Fall, V. Noireaux, R. M. Murray, J. B. Lucks. ACS Synthetic Biology. (2014). doi: 10.1021/sb400206c
Links: Journal, PDF, BioRxiv (Open Access)About
In this paper, an E. coli-based cell free transcription-translation (TX-TL) system is adapted for prototyping RNA genetic networks. This work demonstrates that the response time for an RNA cascade is approximately 5 minute, which allows for more rapid prototyping than protein-based circuits. By prototyping a single input molecule (SIM) RNA circuit in this system, the first in vivo SIM RNA circuit is created and characterized.
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The Centrality of RNA for Engineering Gene Expression
J. Chappell, M. K. Takahashi, S. Meyer, D. Loughrey, K. Watters, J. B. Lucks. Biotechnology Journal. (2013). doi: 10.1002/biot.201300018
Links: Journal, PDFAbout
This review focuses on the role of RNA in synthetic biology and highlights novel methodology for interrogating the form and function relationship of this amazing oligonucleotide. We highlight the numerous RNA regulators of gene expression and delve into methods for engineering synthetic variants. This leads to discussions on combining the power of next-gen sequencing with chemical probing in order to gain insights on RNA structure and how it translates into overall RNA function. This and similar technologies can also be used within the context of the cell to answer fundamental biological questions surrounding cellular RNA.
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A modular strategy for engineering orthogonal chimeric RNA transcription regulators
M. K. Takahashi, J. B. Lucks. Nucleic Acids Research. (2013). doi: 10.1093/nar/gkt452
Links: Journal, PDFAbout
This work develops a set of orthogonal sense-antisense RNA pairs by engineering chimeric attenuators from naturally-occurring translation regulators, expanding the toolkit for RNA genetic circuitry engineering.
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Multiplexed RNA structure characterization with selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
J. B. Lucks*, S. A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G. P. Schroth, L. Pachter, J. A. Doudna*, A. P. Arkin*. PNAS. (2011). (* Co-corresponding author) doi: 10.1073/pnas.1106501108
Links: Journal, PDF
See Commentary! K. M. Weeks. “RNA Structure Probing dash Seq.”, PNAS, 108, 10933, 2011.About
This paper presents the first method to capture nucleotide-resolution structural information for hundreds of RNAs in a single experiment. This method, called SHAPE-Seq, works by merging chemical probing of RNA structures, with next-generation sequencing to read out modification patterns and infer structures. It opened the door to very high throughput RNA structural biology and it and similar techniques are used by laboratories around the world to address fundamental questions in RNA biology and RNA engineering.