Publications
Marcus, A. H.; Matsika, S.; Heussman, D.; Sorour, M. I.; Maurer, J.; Albrecht, C. S.; Enkbaatar, 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. In press. Preprint available at: https://arxiv.org/abs/2403.16251.
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.