AP Site - Explore the Science & Experts | ideXlab

Scan Science and Technology

Contact Leading Edge Experts & Companies

AP Site

The Experts below are selected from a list of 4161 Experts worldwide ranked by ideXlab platform

Olga I. Lavrik – 1st expert on this subject based on the ideXlab platform

  • Quantitative parameters of the 3′–5′ exonuclease reaction of human APurinic/APyrimidinic endonuclease 1 with nicked DNA containing dYMP or a modified dCMP analogue
    Russian Journal of Bioorganic Chemistry, 2020
    Co-Authors: N S Dyrkheeva, Svetlana N. Khodyreva, Olga I. Lavrik

    Abstract:

    Human APurinic/APyrimidinic (AP) endonuclease 1 (APE1) is a multifunctional enzyme. In addition to its main AP endonuclease activity, that incises DNA 5′ to the APSite, it possesses other weak enzymatic activities. One of them is 3′–5′ exonuclease activity, which is most effectively exhibited for DNA duplexes containing modified or mismatched nucleotides at the 3′-end of the primer chain. There is a presumption that APE1 can correct the DNA synthesis catalyzed by DNA polymerase β through the base excision repair process. We determined the quantitative parameters of the 3′–5′ exonuclease reaction in dependence on the reaction conditions to reveal the detailed mechanism of this process. The kinetic parameters of APE1 exonuclease excision of mismatched dCMP and dTMP from the 3′ terminus of single-strand DNA and of photoreactive dCMP analogues APplied for photoaffinity modification of proteins and DNA in recombinant systems and cell/nuclear extracts were determined.

  • interaction of parp 2 with AP Site containing dna
    Biochimie, 2015
    Co-Authors: M M Kutuzov, Svetlana N. Khodyreva, Ekaterina S Ilina, Maria V Sukhanova, Olga I. Lavrik

    Abstract:

    Abstract In eukaryotes the stability of genome is provided by functioning of DNA repair systems. One of the main DNA repair pathways in eukaryotes is the base excision repair (BER). This system requires precise regulation for correct functioning. Two members of the PARP family – PARP-1 and PARP-2, which can be activated by DNA damage – are widely considered as regulators of DNA repair processes, including BER. In contrast to PARP-1, the role of PARP-2 in BER has not been extensively studied yet. Since AP Site is one of the most frequent type of DNA damage and a key intermediate of BER at the stage preceding formation of DNA breaks, in this pAPer we focused on the characterization of PARP-2 interaction with AP Site-containing DNAs. We demonstrated that PARP-2, like PARP-1, can interact with the intact AP Site via Schiff base formation, in spite of crucial difference in the structure of the DNA binding domains of these PARPs. By cross-linking of PARPs to AP DNA, we determined that the N-terminal domains of both PARPs are involved in formation of cross-links with AP DNA. We have also confirmed that DNA binding by PARP-2, in contrast to PARP-1, is not modulated by autoPARylation. PARP-2, like PARP-1, can inhibit the activity of APE1 by binding to AP Site, but, in contrast to PARP-1, this inhibitory influence is hardly regulated by PAR synthesis. At the same time, 5′-dRP lyase activity of both PARPs is comparable, although being much weaker than that of Pol β, which is considered as the main 5′-dRP lyase of the BER process.

  • Effect of multifunctional protein YB-1 on the AP Site cleavage by AP endonuclease 1 and tyrosyl phosphodiesterase 1
    Biopolymers & Cell, 2012
    Co-Authors: P E Pestryakov, Svetlana N. Khodyreva, P. A. Curmi, L. P. Ovchinnikov, Olga I. Lavrik

    Abstract:

    APurinic/APyrimidinic Sites (AP Sites) which represent one of the most abundantly generated DNA lesions in the cell are generally repaired by base excision repair (BER) pathway. Multifunctional protein YB-1 is known to participate in cellular response to genotoxic stress and was shown to interact with several components of BER – DNA glycosylases NTH1, NEIL2, DNA polymerase and DNA ligase III. Therefore, it is of great interest to investigate the influence of YB-1 on one of the major BER enzymes, responsible for AP Site cleavage, AP endonuclease APE1, and on tyrosyl phosphodiesterase Tdp1, participating in APE1 independent pathway of AP Site repair. Aim. Effect of multifunctional protein YB-1 on the AP Site cleavage by the activities of APE1 and Tdp1 was studied. Methods. Gel-mobility shift assays and enzyme activity tests. Results. YB-1 was shown to inhibit the cleavage of AP Site located in single-stranded DNA by both APE1 and Tdp1. Stimulation of APE1 activity on protruding double-stranded DNA in the presence of YB-1 was observed, whereas no effect on Tdp1-mediated cleavage of AP Site in double-stranded DNA was found. Conclusions. YB-1 can modulate the repair of AP Sites in DNA by both positively stimulating APE1 during the classic BER of AP Sites and avoiding a possible generation of doublestrand breaks, arising from the cleavage of single-stranded portion of DNA substrate already used by different DNA-processing pathwa

O I Lavrik – 2nd expert on this subject based on the ideXlab platform

  • AP endonuclease 1 as a key enzyme in repair of APurinic/APyrimidinic Sites
    Biochemistry (Moscow), 2016
    Co-Authors: N S Dyrkheeva, N A Lebedeva, O I Lavrik

    Abstract:

    Human APurinic/APyrimidinic endonuclease 1 (APE1) is one of the key participants in the DNA base excision repair system. APE1 hydrolyzes DNA adjacent to the 5′-end of an APurinic/APyrimidinic (AP) Site to produce a nick with a 3′-hydroxyl group and a 5′-deoxyribose phosphate moiety. APE1 exhibits 3′-phosphodiesterase, 3′-5′-exonuclease, and 3-phosphatase activities. APE1 was also identified as a redox factor (Ref-1). In this review, data on the role of APE1 in the DNA repair process and in other metabolic processes occurring in cells are analyzed as well as the interaction of this enzyme with DNA and other proteins participating in the repair system.

  • poly adp ribose polymerase 1 stimulates the AP Site cleavage activity of tyrosyl dna phosphodiesterase 1
    Bioscience Reports, 2015
    Co-Authors: N A Lebedeva, Maria V Sukhanova, Inna A Vasileva, Nadejda I Rechkunova, Rashid O Anarbaev, O I Lavrik

    Abstract:

    The influence of poly(ADP-ribose)polymerase 1 (PARP1) on the APurinic/APyrimidinic (AP)-Site cleavage activity of tyrosyl–DNA phosphodiesterase 1 (TDP1) and interaction of PARP1 and TDP1 were studied. The efficiency of single or clustered APSite hydrolysis catalysed by TDP1 was estimated. It was shown that the efficiency of APSite cleavage increases in the presence of an additional APSite in the oppoSite DNA strand depending on its position. PARP1 stimulates TDP1; the stimulation effect was abolished in the presence of NAD+. The interaction of these two proteins was characterized quantitatively by measuring the dissociation constant for the TDP1–PARP1 complex using fluorescently-labelled proteins. The distance between the N-termini of the proteins within the complex was estimated using FRET. The data obtained suggest that PARP1 and TDP1 bind in an antiparallel orientation; the N-terminus of the former protein interacts with the C-terminal domain of the latter. The functional significance of PARP1 and TDP1 interaction in the process of DNA repair was demonstrated for the first time.

  • the mechanism of human tyrosyl dna phosphodiesterase 1 in the cleavage of AP Site and its synthetic analogs
    DNA Repair, 2013
    Co-Authors: N A Lebedeva, Alexander A Ishchenko, Murat Saparbaev, Nadejda I Rechkunova, O I Lavrik

    Abstract:

    Abstract The mechanism of hydrolysis of the APurinic/APyrimidinic (AP) Site and its synthetic analogs by using tyrosyl-DNA phosphodiesterase 1 (Tdp1) was analyzed. Tdp1 catalyzes the cleavage of AP Site and the synthetic analog of the AP Site, 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran (THF), in DNA by hydrolysis of the phosphodiester bond between the substituent and 5′ adjacent phosphate. The product of Tdp1 cleavage in the case of the AP Site is unstable and is hydrolyzed with the formation of 3′- and 5′-margin phosphates. The following repair demands the ordered action of polynucleotide kinase phosphorylase, with XRCC1, DNA polymerase β, and DNA ligase. In the case of THF, Tdp1 generates break with the 5′-THF and the 3′-phosphate termini. Tdp1 is also able to effectively cleave non-nucleotide insertions in DNA, decanediol and diethyleneglycol moieties by the same mechanism as in the case of THF cleavage. The efficiency of Tdp1 catalyzed hydrolysis of APSite analog correlates with the DNA helix distortion induced by the substituent. The following repair of 5′-THF and other APSite analogs can be processed by the long-patch base excision repair pathway.

N A Lebedeva – 3rd expert on this subject based on the ideXlab platform

  • AP endonuclease 1 as a key enzyme in repair of APurinic/APyrimidinic Sites
    Biochemistry (Moscow), 2016
    Co-Authors: N S Dyrkheeva, N A Lebedeva, O I Lavrik

    Abstract:

    Human APurinic/APyrimidinic endonuclease 1 (APE1) is one of the key participants in the DNA base excision repair system. APE1 hydrolyzes DNA adjacent to the 5′-end of an APurinic/APyrimidinic (AP) Site to produce a nick with a 3′-hydroxyl group and a 5′-deoxyribose phosphate moiety. APE1 exhibits 3′-phosphodiesterase, 3′-5′-exonuclease, and 3-phosphatase activities. APE1 was also identified as a redox factor (Ref-1). In this review, data on the role of APE1 in the DNA repair process and in other metabolic processes occurring in cells are analyzed as well as the interaction of this enzyme with DNA and other proteins participating in the repair system.

  • poly adp ribose polymerase 1 stimulates the AP Site cleavage activity of tyrosyl dna phosphodiesterase 1
    Bioscience Reports, 2015
    Co-Authors: N A Lebedeva, Maria V Sukhanova, Inna A Vasileva, Nadejda I Rechkunova, Rashid O Anarbaev, O I Lavrik

    Abstract:

    The influence of poly(ADP-ribose)polymerase 1 (PARP1) on the APurinic/APyrimidinic (AP)-Site cleavage activity of tyrosyl–DNA phosphodiesterase 1 (TDP1) and interaction of PARP1 and TDP1 were studied. The efficiency of single or clustered APSite hydrolysis catalysed by TDP1 was estimated. It was shown that the efficiency of APSite cleavage increases in the presence of an additional APSite in the oppoSite DNA strand depending on its position. PARP1 stimulates TDP1; the stimulation effect was abolished in the presence of NAD+. The interaction of these two proteins was characterized quantitatively by measuring the dissociation constant for the TDP1–PARP1 complex using fluorescently-labelled proteins. The distance between the N-termini of the proteins within the complex was estimated using FRET. The data obtained suggest that PARP1 and TDP1 bind in an antiparallel orientation; the N-terminus of the former protein interacts with the C-terminal domain of the latter. The functional significance of PARP1 and TDP1 interaction in the process of DNA repair was demonstrated for the first time.

  • the mechanism of human tyrosyl dna phosphodiesterase 1 in the cleavage of AP Site and its synthetic analogs
    DNA Repair, 2013
    Co-Authors: N A Lebedeva, Alexander A Ishchenko, Murat Saparbaev, Nadejda I Rechkunova, O I Lavrik

    Abstract:

    Abstract The mechanism of hydrolysis of the APurinic/APyrimidinic (AP) Site and its synthetic analogs by using tyrosyl-DNA phosphodiesterase 1 (Tdp1) was analyzed. Tdp1 catalyzes the cleavage of AP Site and the synthetic analog of the AP Site, 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran (THF), in DNA by hydrolysis of the phosphodiester bond between the substituent and 5′ adjacent phosphate. The product of Tdp1 cleavage in the case of the AP Site is unstable and is hydrolyzed with the formation of 3′- and 5′-margin phosphates. The following repair demands the ordered action of polynucleotide kinase phosphorylase, with XRCC1, DNA polymerase β, and DNA ligase. In the case of THF, Tdp1 generates break with the 5′-THF and the 3′-phosphate termini. Tdp1 is also able to effectively cleave non-nucleotide insertions in DNA, decanediol and diethyleneglycol moieties by the same mechanism as in the case of THF cleavage. The efficiency of Tdp1 catalyzed hydrolysis of APSite analog correlates with the DNA helix distortion induced by the substituent. The following repair of 5′-THF and other APSite analogs can be processed by the long-patch base excision repair pathway.