title: Photophysical and dynamical properties of doubly linked Cy3-DNA constructs.
abstract: Photophysical measurements are reported for Cy3-DNA constructs in which both Cy3 nitrogen atoms are attached to the DNA backbone by short linkers. While this linking was thought to rigidify the orientation of the dye and hinder cis-isomerization, the relatively low fluorescence quantum yield and the presence of a short component in the time-resolved fluorescence decay of the dye indicated that cis-isomerization remained possible. Fluorescence correlation spectroscopy and transient absorption experiments showed that photoisomerization occurred with high efficiency. Molecular dynamics simulations of the trans dye system indicated the presence of stacked and unstacked states, and free energy simulations showed that the barriers for stacking/unstacking were low. In addition, simulations showed that the ground cis state was feasible without DNA distortions. Based on these observations, a model is put forward in which the doubly linked dye can photoisomerize in the unstacked state.
authors: Department of Chemistry and Biochemistry and the Biodesign Institute, Arizona State University , PO Box 875601, Tempe, Arizona 85287, United States.
authors: Elana M S
authors: EM
authors: Stennett
authors: Ning
authors: N
authors: Ma
authors: Arjan
authors: A
authors: van der Vaart
authors: Marcia
authors: M
authors: Levitus
mesh_terms: D002232:Carbocyanines / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D055668:Photochemical Processes; D013050:Spectrometry, Fluorescence
chemical_list: D002232:Carbocyanines; C089187:cyanine dye 3; D004247:DNA