PUBLICATIONS & PATENTS
Recent Highlights

RNA‑Stabilized Coat Proteins for Sensitive and Simultaneous Imaging of Distinct Single mRNAs in Live Cells
Kuffner CJ, Marzilli AM, Ngo JT. Accepted, Nature Methods, 2025 (bioRxiv)
Highlights:
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Destabilized MS2 and PP7 coat proteins (dMCP/dPCP) are rapidly degraded and preserved in cells only when bound to cognate hairpins.
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Live-cell imaging of single mRNA molecules ‘background-free'
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Dual-color imaging of distinct mRNA species (MS2- and PP7-tagged)
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Tagged mRNAs can be visualized via coat proteins tagged with single copy fluorescent proteins (mNeonGreen-dMCP)
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Modular and scalable toolset for live cells RNA tracking and synthetic biology.

Fluorescein-Based SynNotch Adaptors for Regulating Gene Expression Responses to Diverse Extracellular and Matrix-Based Cues
Tran JC, Kuffner CJ, Marzilli AM, Miller RE, Silfen ZE, McMahan JB, Sloas CD, Chen CS, Ngo JT. Nature Communications, 2025
Highlights:
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SynNotch receptor with an optimized with a fluorescein-binding domain.
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Chemical control over activation via bio‑orthogonal bond formation.
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Light-induced signal activation for spatial patterning.
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Fluorescein-conjugated ECM-binding peptides for controlling signaling activity based on collagen folding states
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Programmable induction of myogenic-like phenotypes in fibroblasts through controlled ligand chemistry

Tension-Tuned SynNotch Receptors for Synthetic Mechanotransduction and Intercellular Force Detection
Sloas DC, Tran JC, Marzilli AM, Ngo JT. Nature Biotechnology, 2023
Highlights:
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SynNotch receptors fine-tuned tension sensitivities from spanning the physiological piconewton force range (from <12 pN to >54 pN).
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Synthetic Mechanobiology and programmable mechanical “decision-making” circuits: cells differentiate into myogenic lineages in response to specified tension magnitudes.
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Measurement of intercellular force transmission during Notch signaling, quantifying the mechanics of epsin-dependent receptor endocytosis.
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Versatile mechanogenetic toolkit for probing force-mediated biology and engineering force-responsive cellular behaviors.
Publications & Preprints
RNA-Stabilized Coat Proteins for Sensitive and Simultaneous Imaging of Distinct Single mRNAs in Live Cells
Kuffner, C.J., Marzilli, A.M., Ngo, J.T.
Accepted, Nature Methods
Protease-Containing Nanobodies for Detecting and Manipulating Intracellular Antigens Using Antiviral Drugs
Le, Q. and Ngo, J.T.
Fluorescein-Based SynNotch Adaptors for Regulating Gene Expression Responses to Diverse Extracellular and Matrix-Based Cues
Tran, J.C., Kuffner, C.J., Marzilli, A.M., Miller, R.E., Silfen, Z.E., McMahan, J.B., Sloas, C.D., Chen, C.S., Ngo, J.T.
Fe-TAMLs as a new class of small molecule peroxidase probes for correlated light and electron microscopy
Adams, S.R., Mackey, M.R., Ramachandra, R., Deerinck, T.J., Castillon, G.A., Phan, S., Hu, J., Boassa, D., Ngo, J.T., Ellisman, M.H.
Controlled protein activities with viral proteases, antiviral peptides, and antiviral drugs
Tague, E.P., McMahan, J.B., Tague, N., Dunlop, M.B., Ngo, J.T.
Tension-Tuned SynNotch Receptors for Synthetic Mechanotransduction and Intercellular Force Detection
Sloas, D.C., Tran, J.C., Marzilli, A.M., Ngo, J.T.
Nature Biotechnology, 2023, 41: 1287–1295.
SNAP-tag and HaloTag fused proteins for HaSX8-inducible control over synthetic biological functions in engineered mammalian cells.
Dotson, H.L., Ngo, J.T.
Under Review.
A Genetically Encodable and Chemically Disruptable System for Synthetic Post-Translational Modification Dependent Signaling.
McMahan, J.B., Marzilli, A.M., Tran, J.C., Kuffner, C.J., Ngo, J.T.
In Revision.
High-performance multiplex drug-gated CAR circuits.
Li, H,S., Wong, N.M., Tague, E.P., Ngo, J.T., Khalil, A.S., Wong, W.W.
Precision control of intrabodies in live cells. (News and Views)
Marzilli, A.M., McMahan, J.B., Ngo, J.T.
Nature Methods, 2020, 17(3):259–260.
Split-miniSOG for Spatially Detecting Intracellular Protein-Protein Interactions by Correlated Light and Electron Microscopy.
Boassa, D., Lemieux, S.P., Lev-Ram, V., Hu, J., Xiong, Q., Phan, S., Mackey, M., Ramachandra, R., Peace, R.E., Adams, S.R., Ellisman, M.H., Ngo, J.T.
Cell Chemical Biology, 2019, 26(10):1407-1416.e5.
Plasmid #136601 is our reccomended option.
Chemogenetic control of gene expression and cell signaling with antiviral drugs.
Tague, E.P.*, Dotson, H.L.*, Tunney, S.N.*, Sloas, D.C., Ngo, J.T.
Nature Methods, 2018, 15(7):519-522.
PubMed Publisher
Plasmids on AddGene
Commentary in Nature Methods
'Author File' in Nature Methods
Click-electron microscopy for imaging metabolically tagged nonprotein biomolecules.
Ngo, J.T., Adams, S.R., Deerinck, T.J., Boassa, D., Rodriguez-Rivera, F., Palida, S.K., Bertozzi, C.R., Ellisman, M.H., Tsien, R.Y.
Nature Chemical Biology, 2016, 12(6):459-65.
"Greatest Hits" in Nature Chemical Biology
Feature in Cell Chemical Biology
Feature in Angewandte Chemie
PKMζ, But Not PKCλ, Is Rapidly Synthesized and Degraded at the Neuronal Synapse.
Palida, S.F., Butko, M.T., Ngo, J.T., Mackey, M.R., Gross, L.A., Ellisman, M.H., Tsien, R.Y.
Journal of Neuroscience, 2015, 35(20):7736-7749.
Cell-specific proteomic analysis in Caenorhabditis elegans.
Yuet, K.P., Doma, M.K., Ngo, J.T., Sweredoski, M.J., Graham, R.L., Moradian, A., Hess, S., Schuman, E.M., Sternberg, P.W., Tirrell, D.A.
Proc. Natl. Acad. Sci. USA. 2015, 112(9):2705-2710.
Identification of Secreted Bacterial Proteins by Non-Canonical Amino Acid Tagging.
Mahdavi, A., Szychowski, J., Ngo, J.T., Sweredoski, M.J., Graham, R.L.J., Hess, D., Schneewind, O., Mazmanian, S.K., Tirrell, D.A.
Proc. Natl. Acad. Sci. USA. 2014, 111(1):433-438.
Mutant Methionyl-tRNA Synthetase from Bacteria Enables Site-Selective N-terminal Labeling of Proteins Expressed in Mammalian Cells.
Ngo, J.T., Schuman, E.M., Tirrell, D.A.
Proc. Natl. Acad. Sci. USA. 2013, 110(13):4992-4997
State-selective metabolic labeling of cellular proteins.
Ngo, J.T., Babin, B.M., Champion, J.A., Schuman, E.M., Tirrell, D.A.
ACS Chemical Biology, 2012, 7(8):1326-1330.
PubMed
Noncanonical amino acids in the interrogation of cellular protein synthesis.
Ngo, J.T., Tirrell, D.A.
Accounts of Chemical Research, 2011, 44(9):677-685.
Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition.
Szychowski, J., Mahdavi, A., Hodas, J.J., Bagert, J.D., Ngo, J.T., Landgraf, P., Dieterich D.C., Schuman, E.M., Tirrell, D.A.
J. Am. Chem. Soc. 2010, 132(51):18351-18660.
in situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons.
Dieterich, D.C., Hodas, J.J., Gouzer, G., Shadrin, I.Y., Ngo, J.T., Triller, A., Tirrell, D.A., Schuman, E.M.
Nature Neuroscience, 2010, 13(7):897-905.
Cell-selective metabolic labeling of proteins.
Ngo, J.T., Champion, J.A., Mahdavi, A., Tanrikulu, I.C., Beatty, K.E., Connor, R.E., Yoo, T.H., Dieterich, D.C., Schuman, E.M., Tirrell, D.A.
Nature Chemical Biology, 2009, 5(10):715-717.
Unnatural amino acid incorporation into virus-like particles.
Strable, E., Prasuhn, D.E. Jr., Udit, A.K., Brown, S., Link, A.J., Ngo, J.T., Lander, G., Quispe, J., Potter, C.S., Carragher, B., Tirrell, D.A., Finn, M.G.
Bioconjugate Chemistry, 2008, 19(4):866-75.
Commentary, etc.
Precision control of intrabodies in live cells.
Marzilli, A.M., McMahan, Ngo, J.T.
Nature Methods, 2020, 17: 159-260
Patents
SYNTHETIC NOTCH RECEPTOR PROTEIN FOR MODULATING GENE EXPRESSION
United States Patent 12065501, Granted 2024-08-20
Inventor: Ngo, John T.
Assignee: Trustees of Boston University
COMPOSITIONS AND METHODS FOR CONTROLLED MRNA TRANSLATION AND STABILITY
United States Patent Application 20240263193, Published 2024-08-08
Inventors: Marzilli, Alexander Michael, Ngo, John Tuan
Assignee: Trustees of Boston University
ENGINEERED EXTRACELLULAR RECEPTOR CONSTRUCTS AND USES THEREOF
United States Patent 12043652, Granted 2024-07-23
Inventors: Tague, Elliot Parker, Ngo, John T., McMahan, Jeffrey Blye
Assignee: Trustees of Boston University
CELLULAR RECEPTORS AND USES THEREOF
United States Patent 11672828, Granted 2023-06-13
Inventors: Ngo, John T., McMahan, Jeffrey Blye
Assignee: Trustees of Boston University
NOVEL DRUG-CONTROLLED SYSTEMS AND USES THEREOF
United States Patent Application 20220062234, Published 2022-03-03
Inventors: Ngo, John T., Dunlop, Mary, Tague, Elliot Parker, Tague, Nathan Michael, Marzilli, Alexander Michael
Assignee: Trustees of Boston University
INDUCIBLE CELL RECEPTORS FOR CELL-BASED THERAPEUTICS
United States Patent Application 20210189367, Published 2021-06-24
Inventors: Lee, Philip Janmin, Lu, Timothy Kuan-ta, Gordley, Russell Morrison, Wong, Wilson, Ngo, John
Assignees: Senti Biosciences, Inc., Trustees of Boston University
CHIMERIC ANTIGEN RECEPTOR (CAR) MODULATION
United States Patent 11059864, Granted 2021-07-21
Inventors: Ngo, John, Wong, Wilson, Wong, Meng Lai Nicole, Li, Huishan, Tague, Elliot P.
Assignee: Trustees of Boston University
SYNTHETIC NOTCH PROTEIN FOR MODULATING GENE EXPRESSION
United States Patent 10858443, Granted 2020-12-08
Inventor: Ngo, John T.
Assignee: Trustees of Boston University
SYNTHETIC PROTEIN FOR MODULATING GENE EXPRESSION
United States Patent 10717782, Granted 2020-07-21
Inventor: Ngo, John T.
Assignee: Trustees of Boston University