title: Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA.
abstract: Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Addie
authors.initials: A
authors.lastname: Kingsland
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Soumyadyuti
authors.initials: S
authors.lastname: Samai
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Yunqi
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: David S
authors.initials: DS
authors.lastname: Ginger
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Lutz
authors.initials: L
authors.lastname: Maibaum
mesh_terms: D001391:Azo Compounds / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D055668:Photochemical Processes; D011789:Quantum Theory; D013237:Stereoisomerism
chemical_list: D001391:Azo Compounds; D004247:DNA; C009850:azobenzene