A mechanism for DNA-PK activation requiring unique contributions from each strand of a DNA terminus and implications for microhomology-mediated nonhomologous DNA end joining
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DNA-dependent protein kinase (DNA-PK) is an essential component of the nonhomologous end joining pathway (NHEJ), responsible for the repair of DNA double-strand breaks. Ku binds a DSB and recruits the catalytic subunit, DNA-PKcs, where it is activated once the kinase is bound to the DSB. The precise mechanism by which DNA activates DNA-PK remains unknown. We have investigated the effect of DNA structure on DNA-PK activation and results demonstrate that in Ku-dependent DNA-PKcs reactions, DNA-PK activation with DNA effectors containing two unannealed ends was identical to activation observed with fully duplex DNA effectors of the same length. The presence of a 6-base single-stranded extension resulted in decreased activation compared to the fully duplex DNA. DNA-PK activation using DNA effectors with compatible termini displayed increased activity compared to effectors with noncompatible termini. A strand orientation preference was observed in these reactions and suggests a model where the 3' strand of the terminus is responsible for annealing and the 5' strand is involved in activation of DNA-PK. These results demonstrate the influence of DNA structure and orientation on DNA-PK activation and provide a molecular mechanism of activation resulting from compatible termini, an essential step in microhomology-mediated NHEJ.
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Autophosphorylation of DNA-PK occurs when bound to specific sequence composition and DNA termini.
“Autophosphorylation of DNA-PK occurs when bound to specific sequence composition and DNA termini [59,60].”
From Integration of DNA damage and repair with murine double-minute 2 (Mdm2) in tumorigenesis (2012) · cites this paper as [60]
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Cites
Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair
Walker, J. R., Corpina, R. A., & Goldberg, J. D. (2001) · Nature · doi:10.1038/35088000 · Cited by 1,216 · see citing works
Simian virus 40 DNA replication in vitro.
Li, J. J., & Kelly, T. J. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.22.6973 · Cited by 560 · see citing works
Chan, D. W., Chen, B. P.-C., Prithivirajsingh, S., Kurimasa, A., Story, M. D., Qin, J., & Chen, D. J. (2002) · Genes & Development · doi:10.1101/gad.1015202 · Cited by 479 · see citing works
Collis, S. J., DeWeese, T. L., Jeggo, P. A., & Parker, A. R. (2004) · Oncogene · doi:10.1038/sj.onc.1208332 · Cited by 417 · see citing works
Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks
Uematsu, N., Weterings, E., Yano, K., Morotomi‐Yano, K., Jakob, B., Taucher-Scholz, G., Mari, P., van Gent, D. C., Chen, B. P. C., & Chen, D. J. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200608077 · Cited by 414 · see citing works
Lees‐Miller, S. P., Chen, Y. R., & Anderson, C. W. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.12.6472 · Cited by 405 · see citing works
Dvir, A., Peterson, S., Knuth, M. W., Lu, H., & Dynan, W. S. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.24.11920 · Cited by 371 · see citing works
Repair of DNA double strand breaks by non-homologous end joining
Lees‐Miller, S. P. (2003) · Biochimie · doi:10.1016/j.biochi.2003.10.011 · Cited by 367 · see citing works
Synapsis of DNA ends by DNA‐dependent protein kinase
DeFazio, L. G., Stansel, R. M., Griffith, J. D., & Chu, G. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf299 · Cited by 365 · see citing works
Ding, Q., Reddy, Y. V. R., Wang, W., Woods, T. L., Douglas, P., Ramsden, D. A., Lees‐Miller, S. P., & Meek, K. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.16.5836-5848.2003 · Cited by 324 · see citing works
The DNA-dependent Protein Kinase Is Inactivated by Autophosphorylation of the Catalytic Subunit
Chan, D. W., & Lees‐Miller, S. P. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.15.8936 · Cited by 291 · see citing works
Spagnolo, L., Rivera-Calzada, Á., Pearl, L. H., & Llorca, Ó. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.04.013 · Cited by 270 · see citing works
Yoo, S. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.24.4679 · Cited by 228 · see citing works
Human DNA helicase II: a novel DNA unwinding enzyme identified as the Ku autoantigen.
Tuteja, N., Tuteja, R., Ochem, A. E., Taneja, P., Huang, N., Simoncsits, A., Susic, S., Rahman, K., Marusic, L., & Chen, J. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06826.x · Cited by 223 · see citing works
DOUGLAS, P., Sapkota, G. P., MORRICE, N. A., Yu, Y., Goodarzi, A. A., Merkle, D., Meek, K., Alessi, D. R., & Lees‐Miller, S. P. (2002) · Biochemical Journal · doi:10.1042/bj20020973 · Cited by 196 · see citing works
The XRCC4 Gene Product Is a Target for and Interacts with the DNA-dependent Protein Kinase
Leber, R., Wise, T. W., Mizuta, R., & Meek, K. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.3.1794 · Cited by 195 · see citing works
Meek, K., Douglas, P., Cui, X., Ding, Q., & Lees‐Miller, S. P. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.02366-06 · Cited by 193 · see citing works
DNA-dependent protein kinase (Ku protein-p350 complex) assembles on double-stranded DNA.
Suwa, A., Hirakata, M., Takeda, Y., Jesch, S. A., Mimori, T., & Hardin, J. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.15.6904 · Cited by 169 · see citing works
The DNA-dependent protein kinase catalytic subunit phosphorylation sites in human Artemis
Ma, Y., Pannicke, U., Lu, H., Niewolik, D., Schwarz, K., & Lieber, M. R. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m507113200 · Cited by 144 · see citing works
Structure of DNA‐dependent protein kinase: implications for its regulation by DNA
Leuther, K. K., Hammarsten, O., Kornberg, R. D., & Chu, G. (1999) · The EMBO Journal · doi:10.1093/emboj/18.5.1114 · Cited by 127 · see citing works
Wang, H., Guan, J., Wang, H., Perrault, A. R., Wang, Y., & Iliakis, G. E. (2001) · PubMed · Cited by 123 · see citing works
Activation of DNA-dependent Protein Kinase by Single-stranded DNA Ends
Hammarsten, O., DeFazio, L. G., & Chu, G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.3.1541 · Cited by 109 · see citing works
Rivera-Calzada, Á., Maman, J. P., Spagnolo, L., Pearl, L. H., & Llorca, Ó. (2005) · Structure · doi:10.1016/j.str.2004.12.006 · Cited by 107 · see citing works
DNA-PK-dependent phosphorylation of Ku70/80 is not required for non-homologous end joining
Douglas, P., Gupta, S., MORRICE, N. A., Meek, K., & Lees‐Miller, S. P. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.05.003 · Cited by 97 · see citing works
Cisplatin-DNA adducts inhibit translocation of the Ku subunits of DNA-PK
Turchi, J. J. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.23.4634 · Cited by 82 · see citing works
Self-citationKu Stimulation of DNA Ligase IV-dependent Ligation Requires Inward Movement along the DNA Molecule
Kysela, B. P., Doherty, A. J., Chovanec, M., Stiff, T., Ameer‐Beg, S., Vojnovic, B., Girard, P.-M., & Jeggo, P. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303273200 · Cited by 82 · see citing works
Turchi, J. J., & Henkels, K. M. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.23.13861 · Cited by 66 · see citing works
Self-citationPhosphorylation of Artemis following irradiation‐induced DNA damage
Poinsignon, C., de Chasseval, R., Soubeyrand, S., Moshous, D., Fischer, A., Haché, R. J. G., & de Villartay, J. (2004) · European Journal of Immunology · doi:10.1002/eji.200425455 · Cited by 64 · see citing works
Functional Properties of the Separate Subunits of Human DNA Helicase II/Ku Autoantigen
Ochem, A. E., Skopac, D., Costa, M., Rabilloud, T., Vuillard, L. M., Simoncsits, A., Giacca, M., & Falaschi, A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.47.29919 · Cited by 50 · see citing works
Differential activation of DNA-PK based on DNA strand orientation and sequence bias
Pawelczak, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki157 · Cited by 42 · see citing works
Self-citationJovanović, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj504 · Cited by 39 · see citing works
Electron microscopy studies on DNA recognition by DNA-PK
Llorca, Ó., & Pearl, L. H. (2004) · Micron · doi:10.1016/j.micron.2004.05.004 · Cited by 16 · see citing works
Flagged first, then by citations
1 of the 33 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- [32]Hammarsten O DeFazio LG Chu G Activation of DNA-dependent protein kinase by single-stranded DNA ends J. Biol. Chem 2000 275 1541 1550 10636842
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CHIRUVELLA, K. K., Liang, Z., & Wilson, T. E. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012757 · Cited by 377 · see citing works
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Woods, D., & Turchi, J. J. (2013) · Cancer Biology & Therapy · doi:10.4161/cbt.23761 · Cited by 296 · see citing works
Self-citationHammel, M., Yu, Y., Mahaney, B. L., Cai, B., Ye, R., Phipps, B. M., Rambo, R. P., Hura, G. L., Pelikán, M., So, S., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.065615 · Cited by 230 · see citing works
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Liao, H., Wu, J., VanDusen, N. J., Li, Y., & Zheng, Y. (2024) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2024.102344 · Cited by 181 · see citing works
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Yin, X., Liu, M., Tian, Y., Wang, J., & Xu, Y. (2017) · Cell Research · doi:10.1038/cr.2017.110 · Cited by 119 · see citing works
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Chaplin, A. K., Hardwick, S. W., Stavridi, A. K., Buehl, C. J., Goff, N. J., Ropars, V., Liang, S., de Oliveira, T. M., Chirgadze, D. Y., Meek, K., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.005 · Cited by 101 · see citing works
Westhoff, M., Kandenwein, J. A., Karl, S., Vellanki, S. H., Braun, V., Eramo, A., Antoniadis, G., Debatin, K., & Fulda, S. (2009) · Oncogene · doi:10.1038/onc.2009.215 · Cited by 78 · see citing works
Smith, S., Reuven, N. B., Mohni, K. N., Schumacher, A. J., & Weller, S. K. (2014) · Journal of Virology · doi:10.1128/jvi.01723-14 · Cited by 62 · see citing works
Svetlova, M., Solovjeva, L., & Tomilin, N. V. (2009) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2009.08.001 · Cited by 59 · see citing works
Shams, F., Bayat, H., Mohammadian, O., Mahboudi, S., Vahidnezhad, H., Soosanabadi, M., & Rahimpour, A. (2022) · Bioimpacts · doi:10.34172/bi.2022.23871 · Cited by 53 · see citing works
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Self-citation
- Authors
- Pawelczak, K. S., & Turchi, J. J.
- Affiliations
- Indiana University Indianapolis (US)
- Corresponding author
- Turchi, John J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-05-31
- Volume
- 36
- Issue
- 12
- Pages
- 4022-4031
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2475626
- OpenAlex
- W2009896547
- Cited by
- 33
- References
- 33
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2022: 2 · 2021: 2 · 2020: 2 · 2017: 4 · 2016: 1 · 2015: 3 · 2014: 2 · 2013: 3 · 2012: 1
- FWCI
- 1.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by-nc)
- Funders
- Flight Attendant Medical Research Institute
- National Institute for Health and Care Research
- National Institutes of Health
- National Cancer Institute (CA82741, R01CA082741)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Effects of Radiation Exposure
- Keywords
- DNA-dependent protein kinase, Ku protein, non-homologous end joining, DNA double-strand break repair, single-stranded DNA, strand orientation, DNA annealing
- MeSH terms
- DNA, DNA Repair, Enzyme Activation, Models, Biological, Phosphorylation, Sequence Homology, Nucleic Acid, DNA-Activated Protein Kinase
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