48 - Electronic Transition Dipole Moments of Cyanine Dye Labels and Amino-Acid Analogues by Linear Dichroism Spectroscopy
University of Oregon
Fluorescently labeled DNA constructs can be useful spectroscopic probes for biochemical studies of DNA replication and transcription. When two chemically identical chromophores are placed in close proximity within a DNA construct, the electronic properties of the chromophore dimer can provide useful information about local DNA conformations. These types of constructs have been studied using two-dimensional fluorescence spectroscopy (2D-FS) and single-molecule fluorescence-detected linear dichroism (smFLD). Here we use pairs of €internally labeled€ cyanine dyes, which are rigidly inserted into the sugar-phosphate backbone of short double stranded DNA segments. These substrates are used to study local backbone conformational changes during helicase mediated DNA unwinding. In order to interpret spectroscopic signals that depend on the electronic coupling between monomer chromophores, it is necessary to have good working models based on knowledge of the directions and magnitudes of the monomer€s electric dipole transition moments (EDTMs). To this end, we performed linear dichroism (LD) measurements on the Cy3 chromophore in stretched low-density polyethylene films, which allowed us to assign EDTMs to the various features appearing in the monomer absorption spectrum. We have performed similar LD studies of boron-nitrogen indole derivatives, which is an analogue of the amino-acid tryptophan side chain. These analogues have distinct electronic properties that will allow them to be distinguishable from other amino acids side-chains within a protein. This, in turn, provides useful information about the local conformations of the protein.