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Original Articles

Conformational Dynamics of Human AP Endonuclease in Base Excision and Nucleotide Incision Repair Pathways

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Pages 637-652 | Received 16 Oct 2008, Published online: 15 May 2012

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Articles from other publishers (37)

Nikita A. Kuznetsov. (2023) Conformational Dynamics of Biopolymers in the Course of Their Interaction: Multifaceted Approaches to the Analysis by the Stopped-Flow Technique with Fluorescence Detection. Photonics 10:9, pages 1033.
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Yohei Sugimoto, Yuji Masuda, Shigenori Iwai, Yumi Miyake, Rie Kanao & Chikahide Masutani. (2023) Novel mechanisms for the removal of strong replication-blocking HMCES- and thiazolidine-DNA adducts in humans. Nucleic Acids Research 51:10, pages 4959-4981.
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Artemiy S. Bakman, Aleksandra A. Kuznetsova, Lyudmila V. Yanshole, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova & Nikita A. Kuznetsov. (2023) Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase β on the APE1–DNA interaction. DNA Repair 123, pages 103450.
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Artemiy S. Bakman, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova & Nikita A. Kuznetsov. (2022) Pre-steady-state kinetic and mutational insights into mechanisms of endo- and exonuclease DNA processing by mutant forms of human AP endonuclease. Biochimica et Biophysica Acta (BBA) - General Subjects 1866:12, pages 130198.
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Anatoly A. Bulygin, Olga S. Fedorova & Nikita A. Kuznetsov. (2022) Insights into Mechanisms of Damage Recognition and Catalysis by APE1-like Enzymes. International Journal of Molecular Sciences 23:8, pages 4361.
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Anastasiia T. Davletgildeeva, Alexandra A. Kuznetsova, Darya S. Novopashina, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova & Nikita A. Kuznetsov. (2022) Comparative Analysis of Exo- and Endonuclease Activities of APE1-like Enzymes. International Journal of Molecular Sciences 23:5, pages 2869.
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Liudmila A. Abrosimova, Nikita A. Kuznetsov, Natalia A. Astafurova, Anastasiia R. Samsonova, Andrey S. Karpov, Tatiana A. Perevyazova, Tatiana S. Oretskaya, Olga S. Fedorova & Elena A. Kubareva. (2021) Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA. Biomolecules 11:10, pages 1420.
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Alexandra Kuznetsova, Svetlana Senchurova, Alexander Ishchenko, Murat Saparbaev, Olga Fedorova & Nikita Kuznetsov. (2021) Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases. International Journal of Molecular Sciences 22:16, pages 8874.
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Anastasiia T. Davletgildeeva, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova & Nikita A. Kuznetsov. (2021) The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes. Frontiers in Cell and Developmental Biology 9.
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I.V. Alekseeva, A.A. Kuznetsova, A.S. Bakman, O.S. Fedorova & N.A. Kuznetsov. (2020) The role of active-site amino acid residues in the cleavage of DNA and RNA substrates by human apurinic/apyrimidinic endonuclease APE1. Biochimica et Biophysica Acta (BBA) - General Subjects 1864:12, pages 129718.
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Anastasia T. Davletgildeeva, Alexandra A. Kuznetsova, Olga S. Fedorova & Nikita A. Kuznetsov. (2020) Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures. Frontiers in Cell and Developmental Biology 8.
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Anatoly A. Bulygin, Alexandra A. Kuznetsova, Yuri N. Vorobjev, Olga S. Fedorova & Nikita A. Kuznetsov. (2020) The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1. Molecules 25:17, pages 3940.
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Irina V. Alekseeva, Artemiy S. Bakman, Yury N. Vorobjev, Olga S. Fedorova & Nikita A. Kuznetsov. (2019) Role of Ionizing Amino Acid Residues in the Process of DNA Binding by Human AP Endonuclease 1 and in Its Catalysis. The Journal of Physical Chemistry B 123:45, pages 9546-9556.
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Irina V. Alekseeva, Anastasiia T. Davletgildeeva, Olga V. Arkova, Nikita A. Kuznetsov & Olga S. Fedorova. (2019) The impact of single-nucleotide polymorphisms of human apurinic/apyrimidinic endonuclease 1 on specific DNA binding and catalysis. Biochimie 163, pages 73-83.
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Silvia Burra, Daniela Marasco, Matilde Clarissa Malfatti, Giulia Antoniali, Antonella Virgilio, Veronica Esposito, Bruce Demple, Aldo Galeone & Gianluca Tell. (2019) Human AP-endonuclease (Ape1) activity on telomeric G4 structures is modulated by acetylatable lysine residues in the N-terminal sequence. DNA Repair 73, pages 129-143.
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Alexandra A Kuznetsova, Anna G Matveeva, Alexander D Milov, Yuri N Vorobjev, Sergei A Dzuba, Olga S Fedorova & Nikita A Kuznetsov. (2018) Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway. Nucleic Acids Research 46:21, pages 11454-11465.
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Elena S. Dyakonova, Vladimir V. Koval, Alexander A. Lomzov, Alexander A. Ishchenko & Olga S. Fedorova. (2018) Apurinic/apyrimidinic endonuclease Apn1 from Saccharomyces cerevisiae is recruited to the nucleotide incision repair pathway: Kinetic and structural features. Biochimie 152, pages 53-62.
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Alexandra Kuznetsova, Olga Fedorova & Nikita Kuznetsov. (2018) Kinetic Features of 3′-5′ Exonuclease Activity of Human AP-Endonuclease APE1. Molecules 23:9, pages 2101.
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Nadezhda Timofeyeva, Alexandra Ryazanova, Maxim Norkin, Tatiana Oretskaya, Olga Fedorova & Elena Kubareva. (2018) Kinetic Basis of the Bifunctionality of SsoII DNA Methyltransferase. Molecules 23:5, pages 1192.
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Olga A. Kladova, Milena Bazlekowa-Karaban, Sonia Baconnais, Olivier Piétrement, Alexander A. Ishchenko, Bakhyt T. Matkarimov, Danila A. Iakovlev, Andrey Vasenko, Olga S. Fedorova, Eric Le Cam, Barbara Tudek, Nikita A. Kuznetsov & Murat Saparbaev. (2018) The role of the N-terminal domain of human apurinic/apyrimidinic endonuclease 1, APE1, in DNA glycosylase stimulation. DNA Repair 64, pages 10-25.
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N. A. Kuznetsov & O. S. Fedorova. (2016) Thermodynamic analysis of fast stages of specific lesion recognition by DNA repair enzymes. Biochemistry (Moscow) 81:10, pages 1136-1152.
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N. A. Timofeyeva & O. S. Fedorova. (2016) A kinetic mechanism of repair of DNA containing α-anomeric deoxyadenosine by human apurinic/apyrimidinic endonuclease 1. Molecular BioSystems 12:11, pages 3435-3446.
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Anastasia D. Miroshnikova, Alexandra A. Kuznetsova, Yuri N. Vorobjev, Nikita A. Kuznetsov & Olga S. Fedorova. (2016) Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1. Molecular BioSystems 12:5, pages 1527-1539.
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Nikita A. Kuznetsov, Maxim S. Kupryushkin, Tatyana V. Abramova, Alexandra A. Kuznetsova, Anastasia D. Miroshnikova, Dmitry A. Stetsenko, Dmitrii V. Pyshnyi & Olga S. Fedorova. (2016) New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1. Molecular BioSystems 12:1, pages 67-75.
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Elena S. Dyakonova, Vladimir V. Koval, Alexander A. Lomzov, Alexander A. Ishchenko & Olga S. Fedorova. (2015) The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA. Biochimica et Biophysica Acta (BBA) - General Subjects 1850:6, pages 1297-1309.
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Lyubov Yu. Kanazhevskaya, Vladimir V. Koval, Alexander A. Lomzov & Olga S. Fedorova. (2014) The role of Asn-212 in the catalytic mechanism of human endonuclease APE1: Stopped-flow kinetic study of incision activity on a natural AP site and a tetrahydrofuran analogue. DNA Repair 21, pages 43-54.
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Kelly M. Schermerhorn & Sarah Delaney. (2013) Transient-State Kinetics of Apurinic/Apyrimidinic (AP) Endonuclease 1 Acting on an Authentic AP Site and Commonly Used Substrate Analogs: The Effect of Diverse Metal Ions and Base Mismatches. Biochemistry 52:43, pages 7669-7677.
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Anbarasi Kothandapani & Steve M. Patrick. (2013) Evidence for base excision repair processing of DNA interstrand crosslinks. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 743-744, pages 44-52.
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Nikita A. Kuznetsov, Vladimir V. Koval, Dmitry O. Zharkov & Olga S. Fedorova. (2012) Conformational dynamics of the interaction of Escherichia coli endonuclease VIII with DNA substrates. DNA Repair 11:11, pages 884-891.
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Xian-Ying Cheng, Wei-Juan Huang, Shi-Chang Hu, Hai-Lei Zhang, Hao Wang, Jing-Xian Zhang, Hong-Huang Lin, Yu-Zong Chen, Quan Zou & Zhi-Liang Ji. (2012) A Global Characterization and Identification of Multifunctional Enzymes. PLoS ONE 7:6, pages e38979.
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Lyubov Yu. Kanazhevskaya, Vladimir V. Koval, Yury N. Vorobjev & Olga S. Fedorova. (2012) Conformational Dynamics of Abasic DNA upon Interactions with AP Endonuclease 1 Revealed by Stopped-Flow Fluorescence Analysis. Biochemistry 51:6, pages 1306-1321.
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Nadezhda A. Timofeyeva, Vladimir V. Koval, Alexander A. Ishchenko, Murat K. Saparbaev & Olga S. Fedorova. (2011) Lys98 Substitution in Human AP Endonuclease 1 Affects the Kinetic Mechanism of Enzyme Action in Base Excision and Nucleotide Incision Repair Pathways. PLoS ONE 6:9, pages e24063.
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Georgy A. Nevinsky. (2011) Structural, thermodynamic, and kinetic basis for the activities of some nucleic acid repair enzymes. Journal of Molecular Recognition 24:4, pages 656-677.
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N. A. Timofeyeva, V. V. Koval, A. A. Ishchenko, M. K. Saparbaev & O. S. Fedorova. (2011) Kinetic mechanism of human apurinic/apyrimidinic endonuclease action in nucleotide incision repair. Biochemistry (Moscow) 76:2, pages 273-281.
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G. A. Nevinsky. (2011) Main factors providing specificity of repair enzymes. Biochemistry (Moscow) 76:1, pages 94-117.
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Lyubov Yu. Kanazhevskaya, Vladimir V. Koval, Dmitry O. Zharkov, Phyllis R. Strauss & Olga S. Fedorova. (2010) Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair. Biochemistry 49:30, pages 6451-6461.
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Kristina Lakomek, Achim Dickmanns, Elena Ciirdaeva, Lars Schomacher & Ralf Ficner. (2010) Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA. Journal of Molecular Biology 399:4, pages 604-617.
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