title: Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.
abstract: Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Noam S
authors.initials: NS
authors.lastname: Freeman
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Curtis E
authors.initials: CE
authors.lastname: Moore
authors.affiliation: Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg 41296, Sweden.
authors.forename: L Marcus
authors.initials: LM
authors.lastname: Wilhelmsson
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Tor
mesh_terms: D001391:Azo Compounds / Q000737:chemistry; D003562:Cytidine / Q000737:chemistry; D005456:Fluorescent Dyes / Q000138:chemical synthesis* / Q000737:chemistry; D007202:Indicators and Reagents; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009705:Nucleosides / Q000138:chemical synthesis* / Q000737:chemistry; D010777:Photochemistry; D011789:Quantum Theory; D014498:Uracil / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D014529:Uridine / Q000737:chemistry
chemical_list: D001391:Azo Compounds; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D009705:Nucleosides; D014498:Uracil; D003562:Cytidine; C013400:6-aminouracil; D014529:Uridine