Research in the Southern group is in the area of biophysical chemistry. Specifically, our research involves the examination of the conformations of proteins and nucleic acids using fluorescence spectroscopy. Students working in my laboratory will utilize synthetic organic chemistry and molecular biology in order to place fluorescent dye molecules on the system of interest, and then examine the conformations of the protein or nucleic acid using both conventional and single molecule fluorescence spectroscopy. Students performing this research will gain experience with molecular biology techniques, synthesis, spectroscopic instrumentation, lasers and optics, and fluorescence microscopy.

Single Molecule Fluorescence Studies
The proteins we will focus our studies on initially are antibodies. These molecules have an enormous amount of flexibility, which allows them to simultaneously bind antigen molecules and other molecules of the immune system. The interaction of antibodies with other immune system molecules leads to the initiation of an immune response. We will explore the conformational flexibility of antibodies to determine if specific conformations are preferred, and if these conformations enhance the ability of the antibody to bind antigen and other immune system molecules. The specific technique we will use to examine the conformational distribution of the antibodies is fluorescence resonance energy transfer (FRET) at the single molecule level.

FRET involves the use of two dye molecules, a donor and an acceptor, attached at different locations in the system of interest. Electronic excitation of the donor molecule can lead to non-radiative energy transfer to the acceptor, which occurs in a distance-dependent manner. By measuring the efficiency with which energy transfer occurs, the distance between the donor and acceptor molecules can be determined, allowing conformational information to be obtained. Ensemble FRET measurements report only the average conformation present. By performing FRET at the single molecule level, we will determine whether or not conformational subpopulations of the antibodies are present. This work is currently supported by the Camille and Henry Dreyfus Foundation.