Steven Knutson, PhD

ASST PROFESSOR

Accepting Students

734/647-9744

[email protected]

College of Pharmacy
1007 E Huron St
Ann Arbor, MI 48104-1628

5238 Pharm

Knutson Lab

Role Overview and Bio

Steve studied Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and then worked for Thermo Fisher Scientific as an analytical biochemist. He obtained his Ph.D. in Chemistry from Emory University in Atlanta under the mentorship of Jen Heemstra and was recently a Postdoctoral Fellow at Princeton University with David MacMillan. The Knutson laboratory is focused on RNA biochemistry and RNA bioengineering and operates at the intersection of chemical biology, functional genomics, medicinal chemistry, and synthetic biology. We are particularly interested in understanding the complex biology of non-coding RNAs (ncRNAs) and harnessing these insights to engineer next-generation RNA therapeutics.

Research Interests

Non-coding RNA (ncRNA) Biology
A small fraction of the human genome actually encodes proteins (< 2%), yet the majority of it is transcribed into RNA. This landscape of non-coding RNAs (ncRNAs) can function as scaffolds, decoys, guides, and catalysts that can orchestrate cellular behavior. Our lab is fascinated by this frontier. Understanding ncRNA biology holds huge promise for unlocking the complexities of human biology while also inspiring us to engineer new RNA biomedicines.
Proximity Labeling Platforms
Understanding RNA function requires capturing its highly dynamic interactions within the native cellular environment. We develop and deploy advanced proximity labeling techniques to capture RNA-protein, RNA-DNA, and RNA-RNA interactions with high spatial and temporal resolution.
Functional ncRNA Discovery
In our lab, we want to understand which ncRNAs are important, and which parts of them are responsible for their activity. We develop and leverage CRISPR-based functional genomics platform to systematically decode these complex molecules. Using scalable perturbation strategies and advanced screening methodologies to disrupt specific genetic elements, we can map these cause-and-effect relationships across the transcriptome.
RNA Bioengineering
Inspired by the functional potential of non-coding RNAs, our lab is pioneering the design of synthetic RNA biomedicines. We are establishing new directed evolution and synthetic biology platforms to select transcripts with novel bioactivities as well as build generative AI models for designing synthetic RNA biologics from the ground up.

Selected Publications

- Knutson, S. D.*, Morgan, D. C.*, Sloan, J. L., Olsen, J. B., Levine, S., Mintier, G., Sheth, P. R., Kwok, M., MacMillan, D.W.C. Micromap (µMap) photoproximity labeling for integrated phenotypic screening and accelerated prioritization of targeted protein degrader compounds. ChemRxiv, 2026.
- Knutson, S. D.*, Boyer, J. A.*, Morgan, D. C., Großkopf, J., Rabinowitz, J. D., MacMillan, D.W.C. Micromapping (μMap) of HER2 across human breast cancers: photocatalytic proximity labeling identifies primary resistance mechanisms and functional interactors. Nat. Chem. Biol., 2026.
- Knutson, S. D., Pan, R., Bisballe, N., Bloomer, B. J., Raftopolous, P., Saridakis, I., MacMillan, D.W.C. Parallel proteomic and transcriptomic microenvironment mapping (µMap) of nuclear condensates in living cells. J. Am. Chem. Soc., 2024. 147(1), 488-497.
- Pan, R., Knutson, S. D., Huth, S., MacMillan, D.W.C. µMap proximity labeling in living cells reveals stress granule disassembly mechanisms. Nat. Chem. Biol., 2024. 21, 490–500.
- Knutson, S. D., Buksh, B. F., Huth, S., Morgan, D. C., MacMillan, D.W.C. Current advances in photocatalytic proximity labeling. Cell Chem. Biol., 2024. 31(6), 1145-1161.
- Buksh, B. F., Knutson, S. D., Oakley, J. V., Bissonette, N., Oblinsky, D. G., Schwoerer, M., Seath, C. P., Geri, J. B., Scholes, G., Ploss, A., MacMillan, D.W.C. µMap-Red: Proximity labeling by red light photocatalysis. J. Am. Chem. Soc., 2022. 144(14), 6154-6162.
- Knutson, S. D., Arthur, R.A., Johnston, H. R., Heemstra, J. M. Direct immunodetection of global A-to-I RNA editing signatures with a chemiluminescent bioassay. Angew. Chem. Int. Ed., 2021. 60(31), 17009-17017.
- Knutson, S. D.*, Sanford, A. A.*, Swenson, C. S., Korn, M.†, Manuel, B., Heemstra, J. M. Thermoreversible control of nucleic acid function with glyoxal caging. J. Am. Chem. Soc., 2020. 142(41), 17766–17781.
- Knutson, S. D., Arthur, R.A., Johnston, H. R., Heemstra, J. M. Selective enrichment of A-to-I edited transcripts from cellular RNA using Endonuclease V. J. Am. Chem. Soc., 2020. 142(11), 5241-5251.
- Knutson, S. D., Ayele, T. M., Heemstra, J. M. Chemical labeling and affinity capture of inosine-containing RNAs using acrylamidofluorescein. Bioconjug. Chem., 2018, 29(9), 2899-2903.
- Knutson, S. D., Raja, E., Bomgarden, R., Chen, A., Kalyanasundaram, R., Desai, S. Development and evaluation of a fluorescent Antibody-Drug Conjugate for molecular imaging and targeted therapy of pancreatic cancer. PLoS One, 2016, 11.6, e0157762.