Andrew H. Marcus
Education
Andy Marcus received his Ph.D. in physical chemistry from Stanford University in 1994. He was a postdoctoral researcher at the University of Chicago. He joined the faculty of the Department of Chemistry and Biochemistry at the University of Oregon in 1996.
B.A., University of California, San Diego, 1987. Ph.D., Stanford University, 1994 (Advisor: Michael D. Fayer). Postdoctoral: University of Chicago, James Franck Institute, 1994-96 (Advisor: Stuart A. Rice).
Research
The Marcus group works in three primary research areas: i) biophysical studies of nucleic acids and protein-DNA interactions; ii) the development of novel approaches to molecular spectroscopy and imaging, including linear and nonlinear laser spectroscopy and single molecule fluorescence techniques, and iii) the exploration of molecular spectroscopy using quantum light sources. Our studies of the structure and dynamics of macromolecules in biological environments include the diffusive motions and internal structural changes of proteins in membranes and in living cells, as well as the conformational fluctuations of macromolecular machines that interact with and manipulate DNA. To elucidate the conformations of macromolecular complexes, and to monitor their time dependent behavior, we develop and apply spectroscopic methods that are sensitive to the electronic couplings between fluorescent chromophore labels. We also work towards extending these methods to perform experiments at the single-molecule level. Such experiments allow us to study kinetic processes in which biological macromolecules change their local conformations during chemical reactions. In collaboration with UO Chemistry Prof. Peter von Hippel, we are investigating the assembly and functional mechanisms of DNA replication complexes central to gene expression.
Publications
Maurer, J.; Albrecht, C. S.; von Hippel, P. H.; Marcus, A. H., “Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions,” Nucl. Acids Res., 2025. Published online: https://doi.org/10.1093/nar/gkaf047. Preprint available at: https://www.biorxiv.org/content/10.1101/2024.10.27.620477v1.
Sorour, M.; Kistler, K.; Marcus, A. H.; Matsika, S., “Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA,” J. Phys. Chem. B, 2024, 128, 7750-7760. PMCID: PMC11343064. https://pubs.acs.org/doi/10.1021/acs.jpcb.4c03115#.
Marcus, A. H.; Matsika, S.; Heussman, D.; Sorour, M. I.; Maurer, J.; Albrecht, C. S.; Enkhbaatar, L.; Herbert, P.; Kistler, K. A.; von Hippel, P. H., “Spectroscopic Approaches for Studies of Site-Specific DNA Base and Backbone ‘Breathing’ Using Exciton-Coupled Dimer-Labeled DNA.” Invited chapter for Springer Nature book series, Nucleic Acids and Molecular Biology. Volume title: Nucleic Acid Photophysics and Photochemistry. Edited by Spiridoula Matsika and Andrew H. Marcus. Executive editor: Dr. Sabine Schwarz. 2024. See Book: https://link.springer.com/book/9783031688065. Chapter 7: https://link.springer.com/chapter/10.1007/978-3-031-68807-2_7
Albrecht, C. S.; Scatena, L. F.; von Hippel, P. H.; Marcus, A. H., “Two-Photon Excitation Two-Dimensional Fluorescence Spectroscopy (2PE-2DFS) of the Fluorescent Nucleobase 6-MI,” Proc. SPIE, 2024, 12863, 1286305. https://doi.org/10.1117/12.3001802.
Maurer, J.; Albrecht, C. S.; Herbert, P.; Heussman, D.; Chang, A.; von Hippel, P. H.; Marcus, A. H., “Studies of DNA ‘Breathing’ in Exciton-Coupled (iCy3)2 Dimer-Labeled DNA Constructs by Polarization-Sweep Single-Molecule Fluorescence (PS-SMF) Microscopy,” Proc. SPIE, 2024, 12863, 128630C. https://doi.org/10.1117/12.3001962.
Heussman, D.; Enkhbataar, L.; Sorour, M.; Kistler, K.; von Hippel, P. H.; Matsika, S.; Marcus, A. H., “Using Transition Density Models to Interpret Experimental Optical Spectra of Exciton-Coupled Cyanine (iCy3)2 Dimer Probes of Local DNA Conformations At and Near Functional Protein Binding Sites,” (manuscript in review at Nucl. Acids Res., 2024, 52, 2172-1289. https://doi.org/10.1093/nar/gkad1163.
Maurer, J.; Albrecht, C. S.; Herbert, P.; Heussman, D.; Chang, A.; von Hippel, P. H.; Marcus, A. H., “Studies of DNA ‘Breathing’ by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3)2 Dimer-Labeled DNA Fork Constructs,” J. Phys. Chem. B, 2023, 127, 10730-10748. https://pubs.acs.org/doi/full/10.1021/acs.jpcb.3c06463.
Sorour, M.; Marcus, A. H.; Matsika, S. “Unraveling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer,” J. Chem. Phys. A, 2023, 127, 9530-9540. Invited special issue article. https://pubs.acs.org/doi/10.1021/acs.jpca.3c06090.
Marcus, A. H.; Heussman, D.; Maurer, J.; Albrecht, C. S.; Herbert, P., von Hippel, P. H. “Studies of Local DNA Backbone Conformation and Conformational Disorder using Site-Specific Exciton-Coupled Probe Spectroscopy,” Annual Reviews of Physical Chemistry, 2023, 74, 245-265. Invited review article: https://www.annualreviews.org/doi/abs/10.1146/annurev-physchem-090419-041204.
Marcus, A. H.; Raymer, M. G. “JCP Special Topic on Quantum Light in Physical Chemistry and Molecular Spectroscopy,” J. Chem. Phys. 2022. 157, 150401. Invited article for JCP Special Issue, http://doi.org/10.1063/5.0127099.
Sorour, M.; Marcus, A. H.; Matsika, S. “Modeling of Electronic Absorption Spectra of the Indocarbocyanine Dye Cy3,” Molecules, 2022. 27, 4062. https://doi.org/10.3390/molecules27134062.
Heussman, D.; Kittell, J.; von Hippel, P. H.; Marcus, A. H., “Temperature-Dependent Local Conformations and Conformational Heterogeneity of Cyanine Dimer Labeled Single-Stranded – Double-Stranded DNA Junctions by 2D Fluorescence Spectroscopy,” J. Chem. Phys. 2022. 156, 045101-1-23. Invited article for Special Issue on Time-Resolved Vibrational Spectroscopy. https://aip.scitation.org/doi/10.1063/5.0076261. Highlighted as an AIP Scilight Feature Article: https://aip.scitation.org/doi/10.1063/10.0009391, and on the Special Issue Cover: https://aip.scitation.org/action/showLargeCover?doi=10.1063%2Fjcp.2022.156.issue-4.
Sorour, M.; Kistler, K. A.; Marcus, A. H.; Matsika, S. “Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3,” J. Phys. Chem. A, 2021. 125, 7852-7866. Invited article for Special Issue: 125 Years of the Journal of Physical Chemistry. https://doi.org/10.1021/acs.jpca.1c05556.
Israels, B.; Albrecht, C.; Dang, A.; Barney, M.; von Hippel, P. H.; Marcus. A. H. “Sub-Millisecond Conformational Transitions of Single-Stranded DNA Lattices by Photon Correlation Single-Molecule FRET,” J. Phys. Chem. B. 2021.125, 9426-9440. https://pubs.acs.org/doi/full/10.1021/acs.jpcb.1c04119.
Raymer, M. G.; Landes, T.; Marcus, A. H. “Entangled Two-Photon Absorption by Atoms and Molecules: A Quantum Optics Tutorial” J. Chem. Phys., 2021. 155, 081501-1-25. Invited article for Special Issue: Quantum Light Molecular Spectroscopy. https://doi.org/10.1063/5.0049338. Highlighted on the Special Issue Cover. https://aip.scitation.org/action/showLargeCover?doi=10.1063%2Fjcp.2021.155.issue-8.
Landes, T.; Raymer, M. G.; Allgaier, M.; Merkouche, S.; Smith, B. J.; Marcus A. H. “Quantifying the Enhancement of Two-Photon Absorption due to Spectral-Temporal Entanglement,” Optics Express, 2021. 29, 20022-20033. http://doi.org/10.1364/OE.422544.
Raymer, M. G.; Landes, T.; Allgaier, M.; Merkouche, S.; Smith, B. J.; Marcus A. H. “How Large is the Quantum Enhancement by Time-Frequency Entanglement of Photon Pairs?” Optica, 2021. 8, 757-758. https://doi.org/10.1364/OPTICA.426674.
Raymer, M. G.; Landes, T.; Allgaier, M.; Merkouche, S.; Smith, B. J.; Marcus A. H. “Two-Photon Absorption of Molecules by Time-Frequency-Entangled Photon Pairs: The Roles of Photon-Number Correlations and Spectral Correlations.” Published on https://arxiv.org/abs/2012.05375.
Landes, T.; Merkouche, S.; Allgaier, M.; Smith, B. J.; Marcus, A. H.; Raymer, M. G. “Experimental Feasibility of Molecular Two-Photon Absorption with Isolated Time-Frequency-Entangled Photon Pairs,” Physical Review Research, 2021. 3, 033154-1-9. https://doi.org/10.1103/PhysRevResearch.3.033154.
Beyerle, E. R.; Dinpahjooh, M.; Ji, H.; Romano, P. G.; von Hippel, P. H.; Marcus, A. H.; Guenza, M. G. “Dinucleotides as Simple Models of the Base Stacking-Unstacking Component of DNA ‘Breathing’ Mechanisms,” Nucleic Acids Research, 2021. 49, 1872 - 1885. https://doi.org/10.1093/nar/gkab015.
Tamimi, A.; Landes, T.; Lavoie, J.; Raymer, M. G.; Marcus, A. H. “Fluorescence-Detected Fourier Transform Electronic Spectroscopy by Phase-Tagged Photon Counting,” Optics Express, 2020. 28, 25194 – 25214. https://doi.org/10.1364/OE.400245.
Mukamel, S.; Freyberger, M.; Schleich, W.; Bellini, M.; Zavatta, A.; Leuchs, G.; Siberhorn, C.; Boyd, R.; Sanchez Soto, L.; Stefanov, A.; Barbieri, M.; Paterova, A.; Krivitskiy, L.; Shwartz, S.; Tamasaku, K.; Dorfman, K.; Schlawin, F.; Sandoghdar, V.; Raymer, M. G.; Marcus, A. H.; Varnaski, O.; Goodson III, T.; Zhou, Z.; Shi, B.-S.; Asban, S.; Scully, M.; Zhang, Z.; Peng, T.; Vartaniants, I.; del Valle, E.; Laussy, F., “Nonlinear Optical Coherent Spectroscopy with Entangled Photon Pairs” by Michael Raymer and Andrew Marcus, Invited contribution to “Roadmap on Quantum Light Spectroscopy,” Topical Review edited by Shaul Mukamel, J. Phys. B: Atomic, Molecular and Optical Physics, 2020. 53, 72002.
Lavoie, J.; Landes, T.; Tamimi, A.; Smith, B. J.; Marcus, A. H.; Raymer, M. G. “Phase-Modulated Interferometry, Spectroscopy and Refractometry using Entangled Photon-Pairs,” Adv. Quantum Technol., 2020. 1900114-1-15, doi.org/10.1002/qute.201900114.
von Hippel, P. H.; Marcus, A. H. “The Many Roles of Binding Cooperativity in DNA Replication,” Invited New and Notable Commentary for Biophysical Journal, 2019. (Related to Kozlov, Shinn and Lohman Article, Biophysical Journal, 2019, 117, 2120-2140.) Biophysical Journal, 2019. 117, 2043 – 2046, doi.org/10.1016/j.bpj.2019.10.029. PMID: 31708164. PMCID: PMC6895729.
Heussman, D.; Kittell, J.; Kringle, L.; Tamimi, A.; von Hippel, P. H.; Marcus, A. H. “Measuring Local Conformations and Conformational Disorder of (Cy3)2 Dimer Labeled DNA Fork Junctions using Absorbance, Circular Dichroism and Two-Dimensional Fluorescence Spectroscopy” Invited research article from themed collection: Ultrafast Photo-Induced Energy and Charge Transfer, Faraday Discussions, 2019. 216, 211-235. doi: 10.1039/C8FD00245B.
Ji, H.; Johnson, N. P.; von Hippel, P. H.; Marcus, A. H. “Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes,” Biophysical Journal, 2019, 117, 1-15. doi: 10.1016/j.bpj.2019.08.006.
Kringle, L.; Sawaya, N.; Widom, J. R.; Adams, C.; Raymer, M. G.; Aspuru-Guzik, A.; Marcus, A. H., “Temperature-Dependent Conformations of Exciton-Coupled Cy3 Dimers in Double Stranded DNA,” J. Chem. Phys. 2018. 148, 085101-1-13. doi: 10.1063/1.5020084. Selected as an Editor’s Pick and Issue Cover Page Feature Article. PMID: 29495791. PMCID: PMC5826741. https://aip.scitation.org/action/showLargeCover?doi=10.1063%2Fjcp.2018.148.issue-8.
Phelps, C.; Israels, B.; Jose, D.; Marsh, M. C.; von Hippel, P. H.; Marcus, A. H. “Using Microsecond Single-Molecule FRET to Determine the Assembly Pathways of T4 ssDNA Binding Protein onto Model DNA Replication Forks,” Proc. Nat. Acad. Sci. Plus, 2017. 114, E3612-E3621. doi: 10.1073/pnas.1619819114
Phelps, C.; Israels, B.; Jose, D.; Marsh, M. C.; von Hippel, P. H.; Marcus, A. H. “Using Multi-Order Time Correlation Functions (TCFs) to Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments,” J. Phys. Chem. B, 2016. 120, 13003-13016. doi: 10.1021/acs.jpcb.6b08449.
Lee, W.; Gillies, J. P.; Jose, D.; Israels, B. A.; von Hippel, P. H.; Marcus, A. H. “Single-Molecule FRET Studies of the Cooperative and Non-Cooperative Binding Kinetics of the Bacteriophage T4 Single-Stranded DNA Binding Protein (gp32) to ssDNA Lattices at Replication Fork Junctions,” Nucl. Acids Res., 2016, 44, 10691-10710. doi: 10.1093/nar/gkw863.
Karki, K. J.; Kringle, L.; Marcus, A. H.; Pullerits, T. “Phase-synchronous detection of coherent and incoherent nonlinear signals,” J. Optics, 2016, 18, 015504 (7pp).
Johnson, N. P.; Ji, H.; Steinberg, T. H.; von Hippel, P. H.; Marcus, A. H. “Sequence-Dependent Conformational Heterogeneity and Proton Transfer Reactivity of the Fluorescent Guanine Analog 6-Methyl Isoxanthoptherin (6-MI) in DNA,” J. Phys. Chem. B, 2015. Doi: 10.1021/acs.jpcb.5b06361, http://pubs.acs.org/articlesonrequest/AOR-72xqUZqEPbHiih7wPjGK.
Pachón, L. A.; Marcus, A. H.; Aspuru-Guzik, A. “Quantum Process Tomography by 2D Fluorescence Spectroscopy,” J. Chem. Phys., 2015, 142, 212442-1-10. Doi: 10.1063/1.4919954.
Saif, M.; Widom, J. R.; Xu, S.; Abbey, E. R.; Liu, S.-Y.; Marcus, A. H. “Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives,” J. Phys. Chem. B, 2015, 119 (25), 7985-7993. Doi: 10.1021/acs.jpcb.5b03485.
Karke, K. J.; Widom, J. R.; Seibt, J.; Moody, I.; Lonergan, M. C.; Pullerits, T.; Marcus, A. H. “Coherent Two-Dimensional Photocurrent Spectroscopy in a PbS Quantum Dot Photocell,” Nature Communications, 2014, 5, 5869. Doi: 10.1038/ncomms6869.
Lee, W.; von Hippel, P. H.; Marcus, A. H. “Internally labeled Cy3 / Cy5 DNA constructs show greatly enhanced photostability in single-molecule FRET experiments,” Nucleic Acids Research, 2014, 42, 5967 – 5977. doi: 10.1093/nar/gku199.
Raymer, M. R.; Marcus, A. H.; Widom, J. R.; Vitullo, D. L. P. “Entangled photon-pair two dimensional fluorescence spectroscopy (EPP-2DFS),” Prof. Michael D. Fayer Festschrift special issue, guest editors: A. H. Marcus, M. A. Berg, and J. Zheng, J. Phys. Chem. B, 2013, 117, 15559-15575. Doi/10.1021/jp405829n.
Phelps, C.; Lee, W.; Jose, D.; von Hippel, P. H.; Marcus, A. H. “Single-Molecule FRET and Linear Dichroism Studies of DNA ‘Breathing’ and Helicase Binding at Replication Fork Junctions,” Proc. Nat. Acad. Sci., 2013, 110, 17320 – 17325. doi/10.1073/ pnas.1314862110. See also editorial commentary: Fei, J.; Ha, T. “Watching DNA breathe one molecule at a time,” Proc. Nat. Acad. Sci., 2013, 110, 17173 – 17174. doi:10.1073/pnas.1314862110.
von Hippel, P. H.; Johnson, N. P.; Marcus, A. H. “50 Years of DNA ‘Breathing’: Reflections on Old and New Approaches,” special issue of Biopolymers: 50th anniversary of Nucleic Acids Research, Biopolymers, 2013, 99, 923 – 954. Doi:10.1002/bip.22347.
Widom, J. R.; Perdomo-Ortiz, A.; Lee, W.; Rappoport, D.; Molinski, T. F.; Aspuru-Guzik, A.; Marcus, A. H. "Temperature-Dependent Conformations of a membrane supported 'zinc porphyrin tweezer' by 2D Fluorescence Spectroscopy," Invited research article for special issue Prof. John C. Wright Festschrift. J. Phys. Chem. A. 2013, 117, 6171 – 6184. Doi: http://dx.doi.org/10.1021/jp400394zv
Lee, W.; Jose, D.; Phelps, C.; Marcus, A. H; von Hippel, P. H. "A Single-Molecule View of the Assembly Pathway, Subunit Stoichiometry and Unwinding Activity of the Bacteriophage T4 Primosome (Helicase-Primase) Complex," Biochemistry, 2013, 52, 3157 – 3170. http://dx.doi.org/10.1021/bi400231s
Karki, K. J.; Torbjornsson, M.; Widom, J. R.; Marcus, A. H.; Pullerits, T. "Digital Cavities and their Potential Applications," J. Instrumentation, 2013, 8, T05005-1-12. Doi: http://iopscience.iop.org/1748-0221/8/05/T05005
Widom, J. R.; Rappoport, D.; Perdomo-Ortiz, A.; Thomsen, H.; Johnson, N. P.; von Hippel, P. H.; Aspuru-Guzik, A.; Marcus, A. H. “Electronic Transition Moments of 6-Methyl isoxanthoptherin (6-MI) – A Fluorescent Analog of Guanine,” Nucleic Acids Research, 2013, 41, 995 – 1004. Doi:10.1093/nar/gks1148
Sanders, J. N.; Mostame, S.; Saikin, S. K.; Andrade, X.; Widom, J. R.; Marcus, A. H.; Aspuru-Guzik, A. “Compressed Sensing for Multidimensional Spectroscopy Experiments,” J. Phys. Chem. Lett., 2012, 3, 2697-2702.
Perdomo, A.; Widom, J. R.; Lott, G. A.; Aspuru-Guzik, A.; Marcus, A. H. “Conformation and Electronic Population Transfer in Membrane Supported Self-Assembled Porphyrin Dimers by Two-Dimensional Fluorescence Spectroscopy,” J. Phys. Chem. B, 2012, 116, 10757-10770.
Datta, K.; Johnson, N. P.; Villani, G.; Marcus, A. H.; von Hippel, P. H. "Characterization of the 6-Methyl Isoxanthoptherin (6-MI) Base Analogue Dimer, A Spectroscopic Probe for Monitoring Guanine Base Conformation at Specific Sites in Nucleic Acids," Nucl. Acids Res., 2012, 40, 1191-1202.
Lott, G. A.; Perdomo-Ortiz, A.; Utterback, J. K.; Widom, J. R.; Aspuru-Guzik, A.; Marcus, A. H. "Conformation of Self-Assembled Porphyrin Dimers in Liposome Vesicles by Phase-Modulation 2D Fluorescence Spectroscopy," Proc. Nat. Acad. Sci., 2011, 108, 16521-16526.
Senning, E. N.; Marcus, A. H. “Subcellular Dynamics and Protein Conformation Fluctuations Measured by Fourier Imaging Correlation Spectroscopy,” (invited review for Ann. Rev. Phys. Chem., 2010, 61, 111-28.
Senning, E. N.; Marcus, A. H. “Actin Polymerization Driven Mitochondrial Transport in Mating S. cerevisiae,” Proc. Nat. Acad. Sci., 2010. 107, 721-725.
Tekavec, P. F.; Lott, G. A.; Marcus, A. H. “Fluorescence-Detected Two-Dimensional Electronic Coherence Spectroscopy by Acousto-Optic Phase Modulation,” Proceedings of the 16th International Conference (2009), 1060 XVI International Conference on Ultrafast Phenomena, Stresa, Italy (06/09/2008-06/13/2008) Springer, Heidelberg.
Senning, E. N.; Lott, G. A.; Fink, M. C.; Marcus, A. H. “II. Kinetic pathways of switching optical conformations in DsRed by 2D Fourier imaging correlation spectroscopy.” J. Phys. Chem. B 2009, 113, 6854-6860.
Lott, G. A.; Senning, E. N. ; Fink, M. C.; Marcus, A. H. “I. Conformational dynamics of biological macromolecules by polarization-modulated Fourier imaging correlation spectroscopy.” J. Phys. Chem. B 2009, 113, 6847-6853.
Senning, E. N.; Lott, G. A.; Marcus, A. H. “Fourier imaging correlation spectroscopy for studies of intracellular structure-function,” (invited chapter) Meths. Cell Biol. 2008, 90, 117-137.
Fink, M. C.; Marcus A. H. “Simultaneous Measurement of Molecular Anisotropy and Translation by Polarization Modulated MFICS” Philosophical Magazine 2008, 88, 3947-3951.
Tekavec, P. F.; Lott, G. A.; Marcus, A. H. “Fluorescence-Detected Two-Dimensional Electronic Coherence Spectroscopy by Acousto-Optic Phase Modulation,” J. Chem. Phys. 2007, 127, 214307-1-21.
Tekavec, P. F.; Dyke, T. R.; Marcus, A. H. “Wave Packet Interferometry and Quantum State Reconstruction by Acousto-Optic Phase Modulation,” J. Chem. Phys. 2006, 125, 194303-1-19.
Honors and Awards
University of California, San Diego Outstanding Freshman in Chemistry Award, 1983; American Chemical Society Western States Regional Scholar, 1987; American Institute of Chemists Student Research Recognition Foundation Scholar, 1987; Harold Urey Award for Outstanding Excellence in Chemistry, 1987; Provost's Honor List, 1982-1987; Research Corporation Innovation Award, 1997; NSF CAREER Award, 1998; Biophysical Journal "New and Notable" Feature Article, 2000; Innovative Polymer Research Lecturer, National Institutes of Standards and Technology, 2001; University of Wisconsin John L. Schrag Memorial Lectureship, 2014; Fund for Faculty Excellence Award, 2014; Interdisciplinary Research Award, UO Office of Research, Innovation and Graduate Education, 2014; Elected Fellow of the American Physical Society, 2014; Journal of Chemical Physics Editor's Pick and Issue Cover article, 2018; Headline Speaker for Faraday Discussion on Ultrafast Photo-Induced Energy and Charge Transfer, 2019; Journal of Chemical Physics Special Issue Cover Article, 2021; Journal of Chemical Physics Scilight Featured Article and Issue Cover, 2022; Journal of Chemical Physics Editor's Pick, 2022.