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  1. Book: Base excision repair pathway

    Bhakat, Kishor K. / Hazra, Tapas K.

    methods and protocols

    (Methods in molecular biology ; 2701 ; Springer protocols)

    2023  

    Author's details edited by Kishor K. Bhakat, Tapas K. Hazra
    Series title Methods in molecular biology ; 2701
    Springer protocols
    Collection
    Keywords DNA repair
    Subject code 572.86459
    Language English
    Size xiii, 262 Seiten, Illustrationen
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT030343706
    ISBN 9781071633724 ; 9781071633731 ; 1071633724 ; 1071633732
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -2701- not available for loan Lesesaal EG

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  2. Article ; Online: Highly Sensitive Radioactivity-Based DNA 3'-Phosphatase Activity Assay for Polynucleotide Kinase 3'-Phosphatase.

    Chakraborty, Anirban / Hazra, Tapas K

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2701, Page(s) 39–54

    Abstract: Endogenous and exogenous genotoxic agents can generate various types of non-ligatable DNA ends at the site of strand break in the mammalian genome. If not repaired, such lesions will impede transcription and replication and can lead to various cellular ... ...

    Abstract Endogenous and exogenous genotoxic agents can generate various types of non-ligatable DNA ends at the site of strand break in the mammalian genome. If not repaired, such lesions will impede transcription and replication and can lead to various cellular pathologies. Among various "dirty" DNA ends, 3'-phosphate is one of the most abundant lesions generated in the mammalian cells. Polynucleotide kinase 3'-phosphatase (PNKP) is the major DNA end-processing enzyme for resolving 3'-phosphate termini in the mammalian cells, and thus, it is involved in DNA base excision repair (BER), single-strand break repair, and classical nonhomologous end joining (C-NHEJ)-mediated DNA double-strand break (DSB) repair. The 3'-OH ends generated following PNKP-mediated processing of 3'-P are utilized by a DNA polymerase to fill in the gap, and subsequently, the nick is sealed by a DNA ligase to complete the repair process. Here we describe two novel assay systems to detect phosphate release by PNKP's 3'-phosphatase activity and PNKP-mediated in vitro single-strand break repair with minimal repair components (PNKP, DNA polymerase, and DNA ligase) using either purified proteins or cell-free nuclear extracts from mammalian cells/tissues. These assays are highly reproducible and sensitive, and the researchers would be able to detect any significant difference in PNKP's 3'-phosphatase activity as well as PNKP-mediated single-strand break repair activity in diseased mammalian cells/tissues vs normal healthy controls.
    MeSH term(s) Animals ; DNA Repair Enzymes/genetics ; Polynucleotide 5'-Hydroxyl-Kinase/genetics ; Polynucleotide 5'-Hydroxyl-Kinase/metabolism ; Radioactivity ; DNA Repair ; DNA Ligases/metabolism ; DNA-Directed DNA Polymerase/metabolism ; DNA/genetics ; Phosphates ; Phosphoric Monoester Hydrolases/metabolism ; Mammals/genetics
    Chemical Substances DNA Repair Enzymes (EC 6.5.1.-) ; Polynucleotide 5'-Hydroxyl-Kinase (EC 2.7.1.78) ; deoxynucleotide 3'-phosphatase (EC 3.1.3.34) ; DNA Ligases (EC 6.5.1.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; DNA (9007-49-2) ; Phosphates ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2023-08-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3373-1_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Protocols to Measure Oxidative Stress and DNA Damage in Asthma.

    Hosoki, Koa / Chakraborty, Anirban / Hazra, Tapas K / Sur, Sanjiv

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2506, Page(s) 315–332

    Abstract: Asthma is associated with oxidative stress and oxidative damage of biomolecules, including DNA. Here, we describe the protocols to quantify reactive oxygen species (ROS) and oxidative stress markers in a mouse model of allergic airway inflammation. We ... ...

    Abstract Asthma is associated with oxidative stress and oxidative damage of biomolecules, including DNA. Here, we describe the protocols to quantify reactive oxygen species (ROS) and oxidative stress markers in a mouse model of allergic airway inflammation. We also provide detailed methods to measure DNA damage by long-run real-time PCR for DNA-damage quantification (LORD-Q) assay and gene-specific DNA damage analyses by long amplicon (LA)-qPCR. Additionally, we describe methods to quantify oxidized DNA base lesions in lung genomic DNA by mass spectrometry, and to measure enzymatic activity of 8-oxoguanine DNA glycosylase (OGG1). Using these methods, the levels of oxidative stress and DNA damage in allergic inflammation and asthma can be elucidated.
    MeSH term(s) Animals ; Asthma/genetics ; DNA ; DNA Damage ; DNA Repair ; Guanine ; Inflammation ; Mice ; Oxidative Stress ; Reactive Oxygen Species
    Chemical Substances Reactive Oxygen Species ; Guanine (5Z93L87A1R) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2364-0_22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways.

    Islam, Azharul / Chakraborty, Anirban / Sarker, Altaf H / Aryal, Uma K / Pan, Lang / Sharma, Gulshan / Boldogh, Istvan / Hazra, Tapas

    Nucleic acids research

    2024  Volume 52, Issue 5, Page(s) 2416–2433

    Abstract: Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand ... ...

    Abstract Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP's enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.
    MeSH term(s) Animals ; Humans ; Mice ; Acetylation ; DNA Damage ; DNA Repair ; DNA Repair Enzymes/metabolism ; Mammals/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/chemistry ; Polynucleotide 5'-Hydroxyl-Kinase/genetics
    Chemical Substances DNA Repair Enzymes (EC 6.5.1.-) ; Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; Polynucleotide 5'-Hydroxyl-Kinase (EC 2.7.1.78) ; PNKP protein, human (EC 2.7.1.-)
    Language English
    Publishing date 2024-01-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkae002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: DNA glycosylase NEIL2 functions in multiple cellular processes.

    Sarker, Altaf H / Cooper, Priscilla K / Hazra, Tapas K

    Progress in biophysics and molecular biology

    2021  Volume 164, Page(s) 72–80

    Abstract: Cell survival largely depends on the faithful maintenance of genetic material since genomic DNA is constantly exposed to genotoxicants from both endogenous and exogenous sources. The evolutionarily conserved base excision repair (BER) pathway is critical ...

    Abstract Cell survival largely depends on the faithful maintenance of genetic material since genomic DNA is constantly exposed to genotoxicants from both endogenous and exogenous sources. The evolutionarily conserved base excision repair (BER) pathway is critical for maintaining genome integrity by eliminating highly abundant and potentially mutagenic oxidized DNA base lesions. BER is a multistep process, which is initiated with recognition and excision of the DNA base lesion by a DNA glycosylase, followed by DNA end processing, gap filling and finally sealing of the nick. Besides genome maintenance by global BER, DNA glycosylases have been found to play additional roles, including preferential repair of oxidized lesions from transcribed genes, modulation of the immune response, participation in active DNA demethylation and maintenance of the mitochondrial genome. Central to these functions is the DNA glycosylase NEIL2. Its loss results in increased accumulation of oxidized base lesions in the transcribed genome, triggers an immune response and causes early neurodevelopmental defects, thus emphasizing the multitasking capabilities of this repair protein. Here we review the specialized functions of NEIL2 and discuss the consequences of its absence both in vitro and in vivo.
    MeSH term(s) Animals ; DNA ; DNA Damage ; DNA Glycosylases/genetics ; DNA Glycosylases/metabolism ; DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Humans
    Chemical Substances DNA (9007-49-2) ; DNA Glycosylases (EC 3.2.2.-) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
    Language English
    Publishing date 2021-03-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 209302-9
    ISSN 1873-1732 ; 0079-6107
    ISSN (online) 1873-1732
    ISSN 0079-6107
    DOI 10.1016/j.pbiomolbio.2021.03.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.281: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Correction: The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3'-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis.

    Chatterjee, Arpita / Saha, Saikat / Chakraborty, Anirban / Silva-Fernandes, Anabela / Mandal, Santi M / Neves-Carvalho, Andreia / Liu, Yongping / Pandita, Raj K / Hegde, Muralidhar L / Hegde, Pavana M / Boldogh, Istvan / Ashizawa, Tetsuo / Koeppen, Arnulf H / Pandita, Tej K / Maciel, Patricia / Sarkar, Partha S / Hazra, Tapas K

    PLoS genetics

    2024  Volume 20, Issue 1, Page(s) e1011124

    Abstract: This corrects the article DOI: 10.1371/journal.pgen.1004749.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pgen.1004749.].
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1011124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Feeling Stressed under the Sun? RPA1 Acetylation to the Rescue.

    Chakravarti, Debabrata / Hazra, Tapas K

    Cell reports

    2017  Volume 20, Issue 9, Page(s) 1995–1996

    Abstract: Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports, He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage ... ...

    Abstract Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports, He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage response.
    Language English
    Publishing date 2017-08-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2017.08.045
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Site-specific acetylation of polynucleotide kinase 3'-phosphatase (PNKP) regulates its distinct role in DNA repair pathways.

    Islam, Azharul / Chakraborty, Anirban / Sarker, Altaf H / Aryal, Uma K / Sharma, Gulshan / Boldogh, Istvan / Hazra, Tapas

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mammalian polynucleotide kinase 3'-phosphatase (PNKP) is a dual-function DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, which generate 3'-OH and 5'-phosphate termini respectively, as substrates for DNA polymerase and DNA ligase ... ...

    Abstract Mammalian polynucleotide kinase 3'-phosphatase (PNKP) is a dual-function DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, which generate 3'-OH and 5'-phosphate termini respectively, as substrates for DNA polymerase and DNA ligase to complete DNA repair. PNKP is thus involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes, which involve distinct sets of proteins. In this study, we report that PNKP is acetylated at two lysine (K142 and K226) residues. While K142 (AcK142) is constitutively acetylated by p300, CBP acetylates K226 (AcK226) only after DSB induction. Co-immunoprecipitation analysis using antibodies specific for PNKP peptides containing AcK142 or AcK226 of PNKP showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP only with DSBR proteins. Although acetylation at these residues did not significantly affect the enzymatic activity of PNKP
    Language English
    Publishing date 2023-08-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.21.545973
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: NRF2 Regulates Cystathionine Gamma-Lyase Expression and Activity in Primary Airway Epithelial Cells Infected with Respiratory Syncytial Virus.

    Jamaluddin, Mohammad / Haas de Mello, Aline / Tapryal, Nisha / Hazra, Tapas K / Garofalo, Roberto P / Casola, Antonella

    Antioxidants (Basel, Switzerland)

    2022  Volume 11, Issue 8

    Abstract: Cystathionine-y-lyase (CSE) is a critical enzyme for hydrogen sulfide ( ... ...

    Abstract Cystathionine-y-lyase (CSE) is a critical enzyme for hydrogen sulfide (H
    Language English
    Publishing date 2022-08-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704216-9
    ISSN 2076-3921
    ISSN 2076-3921
    DOI 10.3390/antiox11081582
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Feeling Stressed under the Sun? RPA1 Acetylation to the Rescue

    Debabrata Chakravarti / Tapas K. Hazra

    Cell Reports, Vol 20, Iss 9, Pp 1995-

    2017  Volume 1996

    Abstract: Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports, He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage ... ...

    Abstract Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports, He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage response.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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