title: New environment-sensitive multichannel DNA fluorescent label for investigation of the protein-DNA interactions.
abstract: Here, we report the study of a new multichannel DNA fluorescent base analogue 3-hydroxychromone (3HC) to evaluate its suitability as a fluorescent reporter probe of structural transitions during protein-DNA interactions and its comparison with the current commercially available 2-aminopurine (aPu), pyrrolocytosine (Cpy) and 1,3-diaza-2-oxophenoxazine (tCO). For this purpose, fluorescent base analogues were incorporated into DNA helix on the opposite or on the 5'-side of the damaged nucleoside 5,6-dihydrouridine (DHU), which is specifically recognized and removed by Endonuclease VIII. These fluorophores demonstrated different sensitivities to the DNA helix conformational changes. The highest sensitivity and the most detailed information about the conformational changes of DNA induced by protein binding and processing were obtained using the 3HC probe. The application of this new artificial fluorescent DNA base is a very useful tool for the studies of complex mechanisms of protein-DNA interactions. Using 3HC biosensor, the kinetic mechanism of Endonuclease VIII action was specified.
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Alexandra A
authors.initials: AA
authors.lastname: Kuznetsova
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Nikita A
authors.initials: NA
authors.lastname: Kuznetsov
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Yuri N
authors.initials: YN
authors.lastname: Vorobjev
authors.affiliation: Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Nice, France.
authors.forename: Nicolas P F
authors.initials: NP
authors.lastname: Barthes
authors.affiliation: Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Nice, France.
authors.forename: Benoît Y
authors.initials: BY
authors.lastname: Michel
authors.affiliation: Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, CNRS, Nice, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Burger
authors.affiliation: Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia.
authors.forename: Olga S
authors.initials: OS
authors.lastname: Fedorova
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002867:Chromones / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D043224:Deoxyribonuclease (Pyrimidine Dimer) / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding
chemical_list: C479534:3-hydroxychromone; D002867:Chromones; D029968:Escherichia coli Proteins; D005456:Fluorescent Dyes; D004247:DNA; D043224:Deoxyribonuclease (Pyrimidine Dimer)