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 molecular motions to occur. In this talk, I will present fluorescence based nonlinear spectroscopic measurements that determine the three-dimensional shapes, or local conformations, adopted by electronically coupled molecular dimers in biological environments. 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� conformation. 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. I will also describe 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. Such fluctuations may comprise important mechanistic steps on the reaction pathways of a number of biological reactions central to DNA replication and RNA transcription.

Studies of structure and dynamics of protein-DNA complexes by single molecule and 2D fluorescence spectroscopy

248th National Meeting (2014)

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