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Comparative Analysis of Nucleotide Fluorescent Analogs for Registration of DNA Conformational Changes Induced by Interaction with Formamidopyrimidine-DNA Glycosylase Fpg

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Abstract

DNA-substrates containing fluorescent DNA base analogs are widely used to study protein–nucleic acid interactions. In the case of DNA-recognizing enzymes, this approach allows one to register conformational changes in DNA during the formation of enzyme–substrate complexes. An important part of such research is the design of model DNA substrates, which includes both the photophysical properties of the fluorescent groups and their location relative to a specific recognition site, namely, in the same chain on the 5′-, 3′-side or in the complementary chain opposite the specific site. In this work, we report a comparative study of the sensitivity of various fluorescent DNA base analogs, such as 2-aminopurine (aPu), pyrrolocytosine (CPy), 1,3-diaza-2-oxophenoxazine (tCO) and 3-hydroxychromone (3HC), to conformational transformations of DNA in the process of interaction with formamidopyrimidine-DNA glycosylase (Fpg) from Escherichia coli.

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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.

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Authors and Affiliations

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

    A. A. Kuznetsova, O. A. Kladova, 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. Department of Natural Sciences, Novosibirsk State University, 630090, Novosibirsk, Russia

    O. S. Fedorova & N. A. Kuznetsov

Authors
  1. A. A. Kuznetsova
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  2. O. A. Kladova
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  3. Nicolas P. F. Barthes
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  7. N. A. Kuznetsov
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Corresponding authors

Correspondence to O. S. Fedorova or N. A. Kuznetsov.

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The work has no studies involving humans or animals as subjects of the study.

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Translated by N. Onishchenko

Abbreviation: aPu, 2-aminopurine; CPy, pyrrolocytosine; DHU, 5,6-dihydrouracyl; Fpg, formamifopyrimidine-DNA glycosylase; oxoG, 8-oxoguanine; tCO, 1,3-diaza-2-oxofenoxasine; 3HC, 3-hydroxychromone.

Corresponding authors: e-mails: O.S.F., fedorova@ niboch.nsc.ru; nikita.kuznetsov@niboch.nsc.ru.

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Kuznetsova, A.A., Kladova, O.A., Barthes, N.P. et al. Comparative Analysis of Nucleotide Fluorescent Analogs for Registration of DNA Conformational Changes Induced by Interaction with Formamidopyrimidine-DNA Glycosylase Fpg. Russ J Bioorg Chem 45, 591–598 (2019). https://doi.org/10.1134/S1068162019060256

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