title: Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels.
abstract: The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Riedl
authors.forename: Radek
authors.initials: R
authors.lastname: Pohl
authors.forename: Lubomír
authors.initials: L
authors.lastname: Rulíšek
authors.forename: Michal
authors.initials: M
authors.lastname: Hocek
mesh_terms: D015342:DNA Probes / Q000138:chemical synthesis* / Q000737:chemistry; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry; D005456:Fluorescent Dyes / Q000138:chemical synthesis* / Q000737:chemistry; D005461:Fluorine / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D015394:Molecular Structure; D009705:Nucleosides / Q000138:chemical synthesis / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D015342:DNA Probes; D005456:Fluorescent Dyes; D009705:Nucleosides; D005461:Fluorine; D004259:DNA-Directed DNA Polymerase