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New Fluorescent Analogs of Nucleotides Based on 3-Hydroxychromone for Recording Conformational Changes of DNA

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Abstract

It has recently been found that derivatives of nucleotides containing а 3-hydroxychromone fluorescent dye can be used as sensitive markers of conformational changes of DNA. In this work, a comparative analysis of two fluorescent nucleotide derivatives—3-hydroxychromone a (3HC) and 3HC-modified uridine (FCU)—was performed during the study of protein–nucleic acid interactions for several human DNA repair enzymes, removing damaged nucleotides: DNA glycosylases AAG, OGG1, UNG2, and MBD4 and AP endonuclease APE1. The changes of fluorescence intensity significantly depended on the nature of neighbor nucleotides and may be opposite in direction for different cases. The FCU residue located in the complementary strand opposite to damaged nucleotide or in the same strand moved by few nucleotides, is very sensitive to processes induced by DNA glycosylases in the course of formation of enzyme–substrate complexes, which include local melting and bending of the DNA chain, as well as eversion of the damaged nucleotide from DNA double helix and insertion of amino acids of the active site into the void.

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Funding

The work was partially supported by the basic budgetary investment of PFNI GAN 2013-2020, project no. ААА-А17-117020210022-4. Part of the work concerning the analysis of experimental data obtained for human AP endonuclease was supported by the Russian Science Foundation project no. 18-14-00135. Part of the work concerning the analysis of experimental data obtained for DNA glycosylases MBD4 and UNG2 was supported by the Russian Science Foundation project no. 16-14-10038.

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia

    O. A. Kladova, A. A. Kuznetsova, O. S. Fedorova & N. A. Kuznetsov

  2. Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia Antipolis, 06100, Nice, CNRS, France

    Nicolas P. F. Barthes, Benoit Y. Michel & Alain Burger

  3. Novosibirsk State University, 630090, Novosibirsk, Russia

    O. S. Fedorova & N. A. Kuznetsov

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  1. O. A. Kladova
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  2. A. A. Kuznetsova
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  3. Nicolas P. F. Barthes
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  4. Benoit Y. Michel
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  6. O. S. Fedorova
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  7. N. A. Kuznetsov
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Correspondence to O. S. Fedorova or N. A. Kuznetsov.

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Translated by N. Onishchenko

Abbreviations: aPu, 2-aminopurine; CPy, pyrollocytosine; tCO, 1,3-diaza-2-oxophenoxazine; 3-HC, 3-hydroxychromone; FCU, 2-furyl-3-HC-uracyl moiety; F site, 2-hydroxymethyl-3-hydroxytetrahydrofurane; AP site, apurine–apyrimidine site; AAG, alkyladenine-DNA glycosylase; APE1, human AP endonuclease; Hx, hypoxanthine; MBD4, human methylcytosine-binding domain 4; OGG1, human 8-oxoguanine-DNA glycosylase; UNG2, uracyl-DNA glycosylase.

The authors contributed equally to the work.

Corresponding authors: e-mails: fedorova@niboch.nsc.ru; nikita.kuznetsov@niboch.nsc.ru.

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Kladova, O.A., Kuznetsova, A.A., Barthes, N.P. et al. New Fluorescent Analogs of Nucleotides Based on 3-Hydroxychromone for Recording Conformational Changes of DNA. Russ J Bioorg Chem 45, 599–607 (2019). https://doi.org/10.1134/S1068162019060220

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