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Research Interests

RNA Engineering, RNA Folding and Function, Gene Expression Control, Cell-Free Synthetic Biology, Diagnostics

The Lucks Group aims to understand and harness the ability of RNA molecules to control cellular processes for an array of applications in biomanufacturing, diagnostics and disease. Our focus is on making RNA a powerful molecular substrate for engineering gene expression by leveraging its functional versatility, our ability to control its function by designing its structure, and our ability to characterize its biochemistry and biophysics in unprecedented throughput and scale with next generation sequencing tools that we have pioneered. Specifically, we: (1) Engineer new RNA regulatory mechanisms and build RNA genetic networks to precisely program gene expression in applications that range from metabolic engineering to smart diagnostics; and (2) Develop new technologies to uncover RNA sequence/structure/function relationships that feed back into our RNA engineering. We also use our tools to understand natural RNAs that regulate fundamental cellular processes and diseases.

Our research is highly interdisciplinary and links core concepts from chemical engineering, physics, and molecular and structural biology to develop theoretical and experimental techniques for understanding and controlling cellular function with RNAs. To do this we utilize both wet lab and computational techniques. In the wet lab, we use methods spanning molecular biology and biochemistry to next generation RNA sequencing technologies to measure RNA structures in a massively parallel fashion. On the computational side we develop models of RNA genetic networks, develop new techniques for computational RNA design and develop new RNA structure prediction algorithms.

Our current research activities are structured into two thrust areas: (1) Engineering enhanced RNA genetic regulators and networks for control of cellular systems, with a growing interest in using these regulators in cell-free smart diagnostics, and (2) Uncovering the biological design principles of cellular RNA folding and function by developing and applying our SHAPE-Seq technology for measuring RNA structures with next-generation sequencing. These two areas are synergistic, with engineering projects identifying gaps in our knowledge that are filled through fundamental biology investigations.

Education/Academic qualification

Chemical Physics, PhD, Harvard University

… → 2007

Theoretical Chemistry, MPhil, University of Cambridge

… → 2002

Chemical Physics, MS, Harvard University

Chemistry, BS, University of North Carolina

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Grants 2015 2023

Research Output 2002 2019

2 Citations (Scopus)

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control

Strobel, E. J., Cheng, L., Berman, K. E., Carlson, P. D. & Lucks, J. B., Nov 1 2019, In : Nature Chemical Biology. 15, 11, p. 1067-1076 10 p.

Research output: Contribution to journalArticle

Clostridium beijerinckii
Guide RNA
2 Citations (Scopus)

Computational design of three-dimensional RNA structure and function

Yesselman, J. D., Eiler, D., Carlson, E. D., Gotrik, M. R., d’Aquino, A. E., Ooms, A. N., Kladwang, W., Carlson, P. D., Shi, X., Costantino, D. A., Herschlag, D., Lucks, J. B., Jewett, M. C., Kieft, J. S. & Das, R., Sep 1 2019, In : Nature nanotechnology. 14, 9, p. 866-873 8 p.

Research output: Contribution to journalArticle

ribonucleic acids
structural design
13 Citations (Scopus)

Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry

Silverman, A. D., Kelley-Loughnane, N., Lucks, J. B. & Jewett, M. C., Feb 15 2019, In : ACS synthetic biology. 8, 2, p. 403-414 12 p.

Research output: Contribution to journalArticle

Cell Extracts
Transcriptional Activation
Gene expression
Chemical activation
5 Citations (Scopus)

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

Westbrook, A., Tang, X., Marshall, R., Maxwell, C. S., Chappell, J., Agrawal, D. K., Dunlop, M. J., Noireaux, V., Beisel, C. L., Lucks, J. B. & Franco, E., May 1 2019, In : Biotechnology and Bioengineering. 116, 5, p. 1139-1151 13 p.

Research output: Contribution to journalArticle

Pulse generators
Clustered Regularly Interspaced Short Palindromic Repeats
Gene expression

Editorial overview

Lucks, J. B. & Tabor, J. J., Apr 1 2019, In : Current Opinion in Systems Biology. 14, p. iv-vi

Research output: Contribution to journalEditorial