The Center for Excitonics Seminar Series presents

Studies of Structure and Dynamics of Biomolecular Complexes by Single Molecule and Two-Dimensional Fluorescence Spectroscopy (2DFS)

Andrew Marcus
University of Oregon, Department of Chemistry

Thursday, March 20, 2014 / 3pm / 36–428

The properties of biological macromolecules are greatly influenced by local soft interactions between proteins, nucleic acids, sugars and lipids. Such interactions affect the stability of biomolecular complexes, as well as the barriers that must be surmounted for macromolecular machines to function. In this talk, I will present two-dimensional fluorescence spectroscopy (2DFS, a fluorescence-based variant of 2D electronic coherence spectroscopy) to determine the three-dimensional shapes, or local conformations, adopted by electronically coupled molecular dimers in biological systems. I will describe studies of the assembly of dimers of square-shaped metal tetraphenyl porphyrin (TPP) molecules embedded in a phospholipid bilayer membrane, in which we show that the assembled dimers exist as a “T‑shaped” structure. When a flexible linker is used to connect two TPP molecules, the “folded” form of the dimer is favored at elevated temperatures, which we show is due to entropic interactions between the TPP molecules and the local membrane environment. Similar experiments performed on dimers of fluorescent nucleic acid bases, which may be substituted for natural bases within model DNA constructs, reveal the structures of local base stacking conformations, and provide information about the balance of thermodynamic forces that contribute to nucleic acid stability. Finally, I will describe recent single-molecule fluorescence experiments to investigate DNA ‘breathing’ fluctuations, in which nucleotide residues near single-stranded (ss) – double-stranded (ds) DNA forks and junctions temporarily adopt local conformations that depart from their most stable structures. These ‘breathing’ motions occur on microsecond time scales, and are centrally important to the function of DNA-protein complexes responsible for replication, transcription, and other reactions that involve the manipulation of the DNA genome.

Andrew H Marcus is a Professor of Physical Chemistry and member of the Institute for Molecular Biology, Oregon Center for Optics, and Materials Science Institute at the University of Oregon.  He received a B.A. from University of California, San Diego in 1987 and his Ph.D. from Stanford University in 1994 with Michael D. Fayer.   He was a Postdoctoral at the James Franck Institute, University of Chicago from 1994–96 with Stuart A. Rice. He has received the following Honors and Awards: 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; University of California, San Diego Outstanding Freshman in Chemistry; Provost’s Honor List, 1982–1987; Research Corporation Innovation Award, 1997; NSF CAREER Award, 1998.   His research 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.

Related Links:

MIT-Harvard Center for Excitonics

Professor Andrew Marcus