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Stephen C Miller PhD

InstitutionUMass Chan Medical School
DepartmentBiochemistry and Molecular Biotechnology
AddressUMass Chan Medical School
364 Plantation Street LRB
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentPostbaccalaureate Research Education Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentTranslational Science

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentChemical Biology

    Collapse Biography 
    Collapse education and training
    University of Wisconsin, Madison, Madison, WI, United StatesBSChemistry & Biochemistry
    University of California, San Francisco, San Francisco, CA, United StatesPH DMedicinal Chemistry

    Collapse Overview 
    Collapse overview

    Illuminating biological processes with chemistry

    Photo: Stephen Miller

    Our laboratory has two main objectives: 1) non-invasive optical imaging of the intracellular environment with fluorescence and bioluminescence, and 2) spatial and temporal control over protein function. To achieve these goals, we synthesize small molecules that absorb and/or emit light.

    • Optical probes of the intracellular environment

    Fluorescent molecules. Study of the intracellular environment using fluorescence is limited by the inherent absorbance of living tissues. Most optical probes in use today absorb and emit light in the visible wavelength region. Absorption of visible wavelength light by cellular components (e.g., flavins, porphyrins) generates excited state molecules that can give rise to background fluorescence and phototoxicity. In whole animals such as the mouse, absorption of light by the hemoglobin in blood is so great that visible wavelength fluorescence is not viable for imaging.

    Living tissue is most transparent to light beyond the visible range, in a spectral region known as the near-IR (650-900 nm). Although this is the ideal spectral window for any optical probe of living cells or organisms, most near-IR fluorophores are unsuitable for use in the intracellular environment because they either lack cell-permeability or give high-background labeling of cellular organelles and membranes. One of our major goals is the design and application of new near-IR fluorophores and probes that can freely enter living cells and facilitate studies of specific intracellular events.

    Bioluminescent molecules. Luciferase-catalyzed light emission can also be used to report on the intracellular environment, and can be used in live animals such as the mouse. Nonetheless, the properties of luciferase are inherently limited by the ability of the luciferin substrate to access the luciferase, and by its photophysical properties (e.g., emission wavelength). Work in our lab is directed toward the development and optimization of luciferases and luciferins for applications ranging from high-throughput screening to bioluminescence imaging in mice.

    • Photocontrol of protein function

    To exert spatial and temporal control over cellular processes, our lab is using the power of chemistry to synthesize molecules that can block the activation and interactions of specific proteins. Upon irradiation with light, these molecules either fall apart or rearrange to restore protein function. For example, the location and timing of GTPase activation is critical for proper cell function, but is still poorly understood. We will use this photoactivation approach to study these rapid processes in living cells using fluorescence microscopy.

    Collapse Rotation Projects

    Rotation Projects

    Work in our lab uses optical imaging to study live cells and organisms. This multi-disciplinary approach brings together the areas of synthetic organic chemistry, molecular biology, biochemistry and cell biology, with translation into mouse models of disease.

    1) Broadening the scope of bioluminescence: Bioluminescence results from the chemical generation of light that occurs when a luciferase enzyme oxidizes its small molecule luciferin substrate. We have synthesized a wide variety of novel luciferin substrates designed to improve the ability to detect bioluminescence signals. In parallel, we have mutated luciferases to best accommodate these substrates, and have also found that a homologous protein in the fruit fly can act as a luciferase. Projects in the lab range from basic molecular-level biochemical, chemical, and evolutionary studies of luciferases and luciferins, to powerful applications such as imaging of enzyme activity and drug action in the brains of live mice.

    2) Fluorescent probes beyond the visible range: Fluorescent sensors of enzymatic activity, metal ions, and small molecules allow the optical detection of biologically-important molecules. However, most of these sensors are based on visible-wavelength fluorophores that suffer from photoxicity and high background. These probes thus have limited utility in live cells, and are generally unusable in live organisms such as mice. We are designing and constructing sensors that fluoresce in the near-IR, beyond the visible range, which is most suitable for non-invasive optical imaging of the physiological state of live cells and organisms.


    Collapse Post Docs

    Postdoctoral positions are available in the Miller laboratory to investigate and extend the scope of bioluminescence imaging.

    Lab projects range from molecular-level studies of the mechanism of luciferases, to non-invasive imaging of specific biological processes and disease states in live animals. 

    Motivated and inherently curious critical thinkers with backgrounds in biology, chemistry, or both are encouraged to apply.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Mohammad I, Liebmann KL, Miller SC. Firefly luciferin methyl ester illuminates the activity of multiple serine hydrolases. Chem Commun (Camb). 2023 Jul 06; 59(55):8552-8555. PMID: 37337906.
      Citations:    Fields:    
    2. Adams ST, Zephyr J, Bohn MF, Schiffer CA, Miller SC. FruitFire: a luciferase based on a fruit fly metabolic enzyme. bioRxiv. 2023 Jun 30. PMID: 37425765.
    3. Rao DN, Ji X, Miller SC. Silicon functionalization expands the repertoire of Si-rhodamine fluorescent probes. Chem Sci. 2022 May 25; 13(20):6081-6088. PMID: 35685786.
    4. Martin-Burgos B, Wang W, William I, Tir S, Mohammad I, Javed R, Smith S, Cui Y, Arzavala J, Mora D, Smith CB, van der Vinne V, Molyneux PC, Miller SC, Weaver DR, Leise TL, Harrington ME. Methods for Detecting PER2:LUCIFERASE Bioluminescence Rhythms in Freely Moving Mice. J Biol Rhythms. 2022 02; 37(1):78-93. PMID: 34873943.
      Citations: 3     Fields:    Translation:Animals
    5. Ji X, Adams ST, Miller SC. Bioluminescence imaging in mice with synthetic luciferin analogues. Methods Enzymol. 2020; 640:165-183. PMID: 32560797.
      Citations: 5     Fields:    Translation:Animals
    6. Adams ST, Miller SC. Enzymatic promiscuity and the evolution of bioluminescence. FEBS J. 2020 04; 287(7):1369-1380. PMID: 31828943.
      Citations: 7     Fields:    Translation:AnimalsCells
    7. Sharma DK, Adams ST, Liebmann KL, Choi A, Miller SC. Sulfonamides Are an Overlooked Class of Electron Donors in Luminogenic Luciferins and Fluorescent Dyes. Org Lett. 2019 03 15; 21(6):1641-1644. PMID: 30835125.
      Citations: 8     Fields:    Translation:Cells
    8. Vreven T, Miller SC. Computational investigation into the fluorescence of luciferin analogues. J Comput Chem. 2019 01 15; 40(2):527-531. PMID: 30548653.
      Citations: 2     Fields:    Translation:Cells
    9. Choi A, Miller SC. Silicon Substitution in Oxazine Dyes Yields Near-Infrared Azasiline Fluorophores That Absorb and Emit beyond 700 nm. Org Lett. 2018 08 03; 20(15):4482-4485. PMID: 30014702.
      Citations: 6     Fields:    Translation:Cells
    10. Miller SC, Mofford DM, Adams ST. Lessons Learned from Luminous Luciferins and Latent Luciferases. ACS Chem Biol. 2018 07 20; 13(7):1734-1740. PMID: 29439568.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    11. Mofford DM, Liebmann KL, Sankaran GS, Reddy GSKK, Reddy GR, Miller SC. Luciferase Activity of Insect Fatty Acyl-CoA Synthetases with Synthetic Luciferins. ACS Chem Biol. 2017 12 15; 12(12):2946-2951. PMID: 29073357.
      Citations: 6     Fields:    Translation:AnimalsCells
    12. Sharma DK, Adams ST, Liebmann KL, Miller SC. Rapid Access to a Broad Range of 6'-Substituted Firefly Luciferin Analogues Reveals Surprising Emitters and Inhibitors. Org Lett. 2017 11 03; 19(21):5836-5839. PMID: 29039673.
      Citations: 19     Fields:    Translation:Cells
    13. Bandara HMD, Hua Z, Zhang M, Pauff SM, Miller SC, Davie EAC, Kobertz WR. Palladium-Mediated Synthesis of a Near-Infrared Fluorescent K+ Sensor. J Org Chem. 2017 08 04; 82(15):8199-8205. PMID: 28664732.
      Citations: 2     Fields:    Translation:AnimalsCells
    14. Farhood Z, Nguyen SA, Miller SC, Holcomb MA, Meyer TA, Rizk HG. Cochlear Implantation in Inner Ear Malformations: Systematic Review of Speech Perception Outcomes and Intraoperative Findings. Otolaryngol Head Neck Surg. 2017 05; 156(5):783-793. PMID: 28374626.
      Citations: 15     Fields:    Translation:Humans
    15. Choi A, Miller SC. Reductively-labile sulfonate ester protecting groups that are rapidly cleaved by physiological glutathione. Org Biomol Chem. 2017 Feb 07; 15(6):1346-1349. PMID: 28116407.
      Citations: 3     Fields:    Translation:HumansCells
    16. Miller SC, Nguyen SA, Ong AA, Gillespie MB. Transoral robotic base of tongue reduction for obstructive sleep apnea: A systematic review and meta-analysis. Laryngoscope. 2017 01; 127(1):258-265. PMID: 27346300.
      Citations: 15     Fields:    Translation:Humans
    17. Adams ST, Mofford DM, Reddy GS, Miller SC. Firefly Luciferase Mutants Allow Substrate-Selective Bioluminescence Imaging in the Mouse Brain. Angew Chem Int Ed Engl. 2016 Apr 11; 55(16):4943-6. PMID: 26991209.
      Citations: 27     Fields:    Translation:Animals
    18. Mofford DM, Miller SC. Luciferins behave like drugs. ACS Chem Neurosci. 2015 Aug 19; 6(8):1273-5. PMID: 26225810.
      Citations: 12     Fields:    Translation:AnimalsCells
    19. Mofford DM, Adams ST, Reddy GS, Reddy GR, Miller SC. Luciferin Amides Enable in Vivo Bioluminescence Detection of Endogenous Fatty Acid Amide Hydrolase Activity. J Am Chem Soc. 2015 Jul 15; 137(27):8684-7. PMID: 26120870.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    20. Mofford DM, Reddy GR, Miller SC. Aminoluciferins extend firefly luciferase bioluminescence into the near-infrared and can be preferred substrates over D-luciferin. J Am Chem Soc. 2014 Sep 24; 136(38):13277-82. PMID: 25208457.
      Citations: 45     Fields:    Translation:AnimalsCells
    21. Adams ST, Miller SC. Beyond D-luciferin: expanding the scope of bioluminescence imaging in vivo. Curr Opin Chem Biol. 2014 Aug; 21:112-20. PMID: 25078002.
      Citations: 58     Fields:    Translation:Animals
    22. Mofford DM, Reddy GR, Miller SC. Latent luciferase activity in the fruit fly revealed by a synthetic luciferin. Proc Natl Acad Sci U S A. 2014 Mar 25; 111(12):4443-8. PMID: 24616520.
      Citations: 20     Fields:    Translation:AnimalsCells
    23. Evans MS, Chaurette JP, Adams ST, Reddy GR, Paley MA, Aronin N, Prescher JA, Miller SC. A synthetic luciferin improves bioluminescence imaging in live mice. Nat Methods. 2014 Apr; 11(4):393-5. PMID: 24509630.
      Citations: 77     Fields:    Translation:AnimalsCells
    24. Godinat A, Park HM, Miller SC, Cheng K, Hanahan D, Sanman LE, Bogyo M, Yu A, Nikitin GF, Stahl A, Dubikovskaya EA. A biocompatible in vivo ligation reaction and its application for noninvasive bioluminescent imaging of protease activity in living mice. ACS Chem Biol. 2013 May 17; 8(5):987-99. PMID: 23463944.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    25. Pauff SM, Miller SC. A trifluoroacetic acid-labile sulfonate protecting group and its use in the synthesis of a near-IR fluorophore. J Org Chem. 2013 Jan 18; 78(2):711-6. PMID: 23167708.
      Citations: 7     Fields:    
    26. Harwood KR, Mofford DM, Reddy GR, Miller SC. Identification of mutant firefly luciferases that efficiently utilize aminoluciferins. Chem Biol. 2011 Dec 23; 18(12):1649-57. PMID: 22195567.
      Citations: 39     Fields:    Translation:AnimalsCells
    27. Pauff SM, Miller SC. Synthesis of near-IR fluorescent oxazine dyes with esterase-labile sulfonate esters. Org Lett. 2011 Dec 02; 13(23):6196-9. PMID: 22047733.
      Citations: 15     Fields:    Translation:Cells
    28. Rusha L, Miller SC. Design and application of esterase-labile sulfonate protecting groups. Chem Commun (Camb). 2011 Feb 21; 47(7):2038-40. PMID: 21210039.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    29. Reddy GR, Thompson WC, Miller SC. Robust light emission from cyclic alkylaminoluciferin substrates for firefly luciferase. J Am Chem Soc. 2010 Oct 06; 132(39):13586-7. PMID: 20828122.
      Citations: 47     Fields:    Translation:AnimalsCells
    30. Miller SC. Profiling sulfonate ester stability: identification of complementary protecting groups for sulfonates. J Org Chem. 2010 Jul 02; 75(13):4632-5. PMID: 20515067.
      Citations: 12     Fields:    Translation:Cells
    31. Harwood KR, Miller SC. Leveraging a small-molecule modification to enable the photoactivation of rho GTPases. Chembiochem. 2009 Dec 14; 10(18):2855-7. PMID: 19877002.
      Citations: 2     Fields:    
    32. Bhunia AK, Miller SC. Labeling tetracysteine-tagged proteins with a SplAsH of color: a modular approach to bis-arsenical fluorophores. Chembiochem. 2007 Sep 24; 8(14):1642-5. PMID: 17694522.
      Citations: 12     Fields:    Translation:Cells
    33. Miller SC, Mitchison TJ. Synthesis and phenotypic screening of a Guanine-mimetic library. Chembiochem. 2004 Jul 05; 5(7):1010-2. PMID: 15239063.
      Citations:    Fields:    Translation:HumansCells
    34. Miller SC, Scanlan TS. oNBS-SPPS: A New Method for Solid-Phase Peptide Synthesis. J. Am. Chem. Soc. 1998; 120:2690-1.
    35. Miller SC, Scanlan TS. Site-Selective N-Methylation of Peptides on Solid Support. J. Am. Chem. Soc. 1997; 119:2301-2.
    36. Truckses DM, Somoza JR, Prehoda KE, Miller SC, Markley JL. Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease. Protein Sci. 1996 Sep; 5(9):1907-16. PMID: 8880915.
      Citations: 17     Fields:    Translation:Cells
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