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Russian Journal of Bioorganic Chemistry

, Volume 45, Issue 6, pp 591–598 | Cite as

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

  • A. A. Kuznetsova
  • O. A. Kladova
  • Nicolas P. F. Barthes
  • Benoit Y. Michel
  • Alain Burger
  • O. S. FedorovaEmail author
  • N. A. KuznetsovEmail author
Article
  • 18 Downloads

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.

Keywords:

DNA glycosylase Fpg conformational dynamics fluorescence protein–nucleic acid interactions 

Notes

FUNDING

The work was partially supported by the basic budgetary investment of PFNI GAN 2013-2020, project no. ААА-А17-117020210022-4.

COMPLIANCE WITH ETHICAL STANDARDS

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

Conflict of Interest

Authors declare they have no conflicts of interest.

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Copyright information

© Pleiades Publishing, Ltd. 2019

Authors and Affiliations

  • A. A. Kuznetsova
    • 1
  • O. A. Kladova
    • 1
  • Nicolas P. F. Barthes
    • 2
  • Benoit Y. Michel
    • 2
  • Alain Burger
    • 2
  • O. S. Fedorova
    • 1
    • 3
    Email author
  • N. A. Kuznetsov
    • 1
    • 3
    Email author
  1. 1.Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of SciencesNovosibirskRussia
  2. 2.Institut de Chimie de Nice, UMR 7272, Université de Nice Sophia AntipolisNiceFrance
  3. 3.Department of Natural Sciences, Novosibirsk State UniversityNovosibirskRussia

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