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2013 Chemistry Newsletter
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2013 Beckman Scholars Program
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The Marcus group studies the structure and dynamics of macromolecules in biological environments. These 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 linear and nonlinear spectroscopic methods that are sensitive to the electronic couplings between fluorescent chromophore labels. Spectroscopic characterization of exciton-coupled dimer probes, which are attached at specific locations on the macromolecules, allows us to observe functionally important macromolecular conformations. For example, by using fluorescent nucleic acid analogues placed at sites near the forks and junctions of primer-template DNA, we study the effects of protein-DNA interactions on local base-stacking conformation. In collaboration with UofO Prof. Peter von Hippel, we are investigating the mechanisms of polymerase and helicase, two protein-DNA complexes central to gene expression. Extension of our techniques to single molecule fluorescence imaging allows us to observe bio-molecular events in real time.
Molecular studies of how protein machines enact and regulate gene expression are critical to understand the chemical basis of life processes.
We developed phase-modulation two-dimensional fluorescence spectroscopy (PM-2D FS) to characterize the exciton-coupling of dimer probes, and to determine dimer conformation. These experiments yield two-dimensional optical spectra, which in analogy to two-dimensional nuclear magnetic resonance (2D NMR), provide information about the couplings between molecular electronic states.
The PM-2D FS instrument (above) produces sequences of tunable ultrafast optical pulses (schematically represented below).
The conformation of molecular complexes are determined by comparing the results of computer simulated models to experimental PM-2D FS data.
University of Oregon graduate student Eric Senning (left) and undergraduate Jimmy Utterback (right) prepare single-molecule fluorescence instrumentation.
Marcus and von Hippel combined group photo. From left to right. Back row: John Gillies, Huiying Ji, Carey Phelps, Julia Widom, Susan Scott, Pete von Hippel, Brett Isreals, Steve Weitzel, Tom Steinberg, Davis Jose, Neil Johnson, Andy Marcus. Front row: Loni Kringle, Rocky (the dog), Mari Saif, Wonbae Lee.
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/jp400394z
Widom, J. R.; Johnson, N. P.; von Hippel, P. H.; Marcus, A. H. "Solution Conformation of 2-Aminopurine (2-AP) Dinucleotide by Ultraviolet 2D Fluorescence Spectroscopy (UV-2D FS)," Invited research article for special issue on 2D optical coherence spectroscopy, New J. Phys., 2013, 15, 025028-1-16. http://dx.doi.org/10.1021/jp400394z
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," Journal of Instrumentation, 2013, 8, T05005-1-12. Doi: http://iopscience.iop.org/1748-0221/8/05/T05005
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 (in press, accepted July 2, 2013).
Phelps, C.; Lee, W.; Jose, D.; von Hippel; Marcus, A. H. "Single-Molecule FRET and Linear Dichroism Studies of DNA ‘Breathing’ and Helicase Binding at Replication Fork Junctions," Proc. Nat. Acad. Sci. (in press, accepted July 26, 2013.
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. Selected for publication in the January 2007 issue of the Virtual Journal of Ultrafast Science (see: www.vjultrafast.org).
Goulding, M. B.; Canman, J. C.; Senning, E. N.; Marcus, A. H.; Bowerman, B. “Control of Nuclear Centration in the C. elegans Zygote by Receptor-Independent G Signaling and Myosin II,” J. Cell Biol. 2007, 178, 1177-1191.
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. Selected for publication in the December 2006 issue of the Virtual Journal of Ultrafast Science (see: www.vjultrafast.org).
Fink, M. C.; Adair, K. V.; Guenza, M. G.; Marcus, A. H. “Translational Diffusion of Fluorescent Proteins by Molecular Fourier Imaging Correlation Spectroscopy,” Biophys. J. 2006, Volume 91, 3482-3498.
Knowles, M. K.; Honerkamp-Smith, A. R.; Marcus, A. H. “Direct Measurement of the Relative and Collective Diffusion in a Dilute Binary Suspension of Colloidal Particles,” J. Chem. Phys. 2005, 122, 234909-1-13.
Knowles, M. K., M. G. Guenza, R. A. Capaldi, and A. H. Marcus, "Cytoskeletal-assisted dynamics of the mitochondrial reticulum in living cells." Proc. Nat. Acad. Sci. 2002, 99, 14772-14777.
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