title: Photoisomerization quantum yield of azobenzene-modified DNA depends on local sequence.
abstract: Photoswitch-modified DNA is being studied for applications including light-harvesting molecular motors, photocontrolled drug delivery, gene regulation, and optically mediated assembly of plasmonic metal nanoparticles in DNA-hybridization assays. We study the sequence and hybridization dependence of the photoisomerization quantum yield of azobenzene attached to DNA via the popular d-threoninol linkage. Compared to free azobenzene we find that the quantum yield for photoisomerization from trans to cis form is decreased 3-fold (from 0.094 ± 0.004 to 0.036 ± 0.002) when the azobenzene is incorporated into ssDNA, and is further reduced 15-fold (to 0.0056 ± 0.0008) for azobenzene incorporated into dsDNA. In addition, we find that the quantum yield is sensitive to the local sequence including both specific mismatches and the overall sequence-dependent melting temperature (Tm). These results serve as design rules for efficient photoswitchable DNA sequences tailored for sensing, drug delivery, and energy-harvesting applications, while also providing a foundation for understanding phenomena such as photonically controlled hybridization stringency.
authors.affiliation: Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Yunqi
authors.initials: Y
authors.lastname: Yan
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.forename: Jennifer I L
authors.initials: JI
authors.lastname: Chen
authors.forename: David S
authors.initials: DS
authors.lastname: Ginger
mesh_terms: D001391:Azo Compounds / Q000737:chemistry*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D055668:Photochemical Processes; D011789:Quantum Theory; D017422:Sequence Analysis, DNA; D013237:Stereoisomerism; D044366:Transition Temperature
chemical_list: D001391:Azo Compounds; D004247:DNA; C009850:azobenzene