Research Interests

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).

Ultraviolet femtosecond optical pulses are used to excite analog labeled DNA molecules in solution, and the fluorescence is monitored in a PM-2D FS experiment.

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.