title: Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout.
abstract: By using (S)-2-amino-1,3-propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady-state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts. Time-resolved pump-probe measurements and excitation spectra reveal the coexistence of conformations, including mainly stacked TO dimers and partially unstacked ones, which yield exciton and excimer contributions to the fluorescence, respectively. The helicity of the DNA framework distorts the excitonic coupling. In particular, the interstrand TO dimer could be regarded as an excitonically interacting base pair with fluorescence readout for DNA hybridization. Finally, the use of this fluorescent readout was representatively demonstrated in molecular beacons.
authors.affiliation: Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.|Institute of Organic Chemistry, University of Regensburg, 93040, Regensburg, Germany.
authors.forename: Sina
authors.initials: S
authors.lastname: Berndl
authors.affiliation: Centre for Plastic Electronics, Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
authors.forename: Stoichko D
authors.initials: SD
authors.lastname: Dimitrov
authors.affiliation: Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.|Institute of Organic Chemistry, University of Regensburg, 93040, Regensburg, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Menacher
authors.affiliation: Feinberg School of Medicine, Department of Otolaryngology, Northwestern University, 420 East Superior Street, Chicago, IL, 60611, USA.
authors.forename: Torsten
authors.initials: T
authors.lastname: Fiebig
authors.affiliation: Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany. Wagenknecht@kit.edu.|Institute of Organic Chemistry, University of Regensburg, 93040, Regensburg, Germany. Wagenknecht@kit.edu.
authors.forename: Hans-Achim
authors.initials: HA
authors.lastname: Wagenknecht
mesh_terms: D001483:Base Sequence; D052160:Benzothiazoles / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000737:chemistry*; D011412:Propanolamines / Q000737:chemistry*; D011409:Propylene Glycols / Q000737:chemistry*; D011804:Quinolines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D052160:Benzothiazoles; D005456:Fluorescent Dyes; D009696:Nucleic Acids; D011412:Propanolamines; D011409:Propylene Glycols; D011804:Quinolines; C051000:thiazole orange; D004247:DNA; C072422:serinol
keywords: DNA; chromophores; dyes/pigments; fluorescence; nucleic acids