Differential activation of DNA-PK based on DNA strand orientation and sequence bias
Open accessAbstract
DNA-PKcs and Ku are essential components of the complex that catalyzes non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Ku, a heterodimeric protein, binds to DNA ends and facilitates recruitment of the catalytic subunit, DNA-PKcs. We have investigated the effect of DNA strand orientation and sequence bias on the activation of DNA-PK. In addition, we assessed the effect of the position and strand orientation of cisplatin adducts on kinase activation. A series of duplex DNA substrates with site-specific cisplatin-DNA adducts placed in three different orientations on the duplex DNA were prepared. Terminal biotin modification and streptavidin (SA) blocking was employed to direct DNA-PK binding to the unblocked termini with a specific DNA strand orientation and cisplatin-DNA adduct position. DNA-PK kinase activity was measured and the results reveal that DNA strand orientation and sequence bias dramatically influence kinase activation, only a portion of which could be attributed to Ku-DNA binding activity. In addition, cisplatin-DNA adduct position resulted in differing degrees of inhibition depending on distance from the terminus as well as strand orientation. These results highlight the importance of how local variations in DNA structure, chemistry and sequence influence DNA-PK activation and potentially NHEJ.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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 [59]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Carney, J. P., Maser, R. S., Olivares, H., Davis, E. M., Le Beau, M., Yates, J. R., Hays, L., Morgan, W. F., & Petrini, J. H. J. (1998) · Cell · doi:10.1016/s0092-8674(00)81175-7 · Cited by 1,226 · see citing works
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
Ma, Y., Pannicke, U., Schwarz, K., & Lieber, M. R. (2002) · Cell · doi:10.1016/s0092-8674(02)00671-2 · Cited by 1,166 · see citing works
The 3′ to 5′ Exonuclease Activity of Mre11 Facilitates Repair of DNA Double-Strand Breaks
Paull, T. T., & Gellert, M. F. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80097-0 · Cited by 919 · see citing works
Moshous, D., Callebaut, I., de Chasseval, R., Corneo, B., Cavazzana, M., Deist, F. L., Tezcan, İ., Sanal, Ö., Bertrand, Y., Philippe, N., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00309-9 · Cited by 912 · see citing works
Nuclease Activities in a Complex of Human Recombination and DNA Repair Factors Rad50, Mre11, and p95
Trujillo, K. M., Yuan, S. F., Lee, E. Y.-H. P., & Sung, P. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.34.21447 · Cited by 417 · see citing works
Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends
McElhinny, S. A. N., McCarville, J., Snowden, C. M., & Ramsden, D. A. (2020) · PubMed Central · doi:10.17615/5hds-gb46 · Cited by 402 · 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
Blier, P. R., Griffith, A. J., Craft, J. E., & Hardin, J. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)53216-6 · Cited by 327 · see citing works
High mobility group protein-1 (HMG-1) is a unique activator of p53Preprint
Jayaraman, L., Moorthy, N. C., Murthy, K. G. K., Manley, J. L., Bustin, M., & Prives, C. L. (1998) · Genes & Development · doi:10.1101/gad.12.4.462 · Cited by 319 · see citing works
Gelasco, A. K., & Lippard, S. J. (1998) · Biochemistry · doi:10.1021/bi973176v · Cited by 284 · see citing works
ATM, ATR and DNA-PK: initiators of the cellular genotoxic stress responses
Yang, H. J. (2003) · Carcinogenesis · doi:10.1093/carcin/bgg137 · Cited by 275 · see citing works
Yoo, S. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.24.4679 · Cited by 228 · see citing works
Vaisman, A., Lim, S. E., Patrick, S. M., Copeland, W. C., Hinkle, D. C., Turchi, J. J., & Chaney, S. G. (1999) · Biochemistry · doi:10.1021/bi9909187 · Cited by 137 · 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
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
Photocross-linking of an Oriented DNA Repair Complex
Yoo, S., Kimzey, A. L., & Dynan, W. S. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.28.20034 · Cited by 91 · 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
Ku Selectively Transfers between DNA Molecules with Homologous Ends
Bliss, T. M., & Lane, D. P. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.9.5765 · Cited by 78 · see citing works
Visualization of DNA‐induced conformational changes in the DNA repair kinase DNA‐PKcs
Boskovic, J., Rivera-Calzada, Á., Maman, J. D., Chacón, P., Willison, K. R., Pearl, L. H., & Llorca, Ó. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg555 · Cited by 73 · 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
DNA-dependent Protein Kinase Catalytic Subunit
Mårtensson, S., & Hammarsten, O. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m106711200 · Cited by 55 · see citing works
Andrews, B. J., & Turchi, J. J. (2004) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.385.3.4 · Cited by 47 · see citing works
The DNA-activated protein kinase, DNA-PK: a potential coordinator of nuclear events.
Lees‐Miller, S. P., & Anderson, C. W. (1991) · PubMed · Cited by 42 · see citing works
Mechanism of DNA-Dependent Protein Kinase Inhibition by cis-Diamminedichloroplatinum(II)-Damaged DNA
Turchi, J. J., Patrick, S. M., & Henkels, K. M. (1997) · Biochemistry · doi:10.1021/bi963124q · Cited by 40 · see citing works
DNA adducts of cisplatin, transplatin and platinum-intercalating drugs.
Leng, M., & Brabec, V. (1994) · PubMed · Cited by 26 · see citing works
Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends
McElhinny, S. A. N., Snowden, C. M., McCarville, J., & Ramsden, D. A. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.9.2996-3003.2000 · Cited by 9 · see citing works
Homologous Recombination, Non-Homologous End-Joining and Cell Cycle: Genomes Angels
Delacôte, F., Guirouilh‐Barbat, J., Lambert, S., & López, B. S. (2004) · Current Genomics · doi:10.2174/1389202043490041 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Repair of Double-Strand Breaks by End JoiningPreprint
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
Thompson, L. H. (2012) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2012.06.002 · Cited by 357 · see citing works
DNA‐PK autophosphorylation facilitates Artemis endonuclease activity
Goodarzi, A. A., Yu, Y., Riballo, E., Douglas, P., Walker, S. A., Ye, R., Härer, C. J., Marchetti, C., MORRICE, N. A., Jeggo, P. A., et al. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601255 · Cited by 342 · see citing works
Meek, K., Dang, V. D., & Lees‐Miller, S. P. (2008) · Advances in immunology · doi:10.1016/s0065-2776(08)00602-0 · Cited by 271 · see citing works
Cisplatin Sensitizes Cancer Cells to Ionizing Radiation via Inhibition of Nonhomologous End Joining
Boeckman, H. J., Trego, K. S., & Turchi, J. J. (2005) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-04-0032 · Cited by 173 · see citing works
Modulating DNA Repair Pathways to Improve Precision Genome Engineering
Pawelczak, K. S., Gavande, N. S., VanderVere-Carozza, P. S., & Turchi, J. J. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00777 · Cited by 132 · see citing works
Processing of DNA for nonhomologous end‐joining by cell‐free extract
Budman, J., & Chu, G. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600563 · Cited by 121 · see citing works
Cryo-EM of NHEJ supercomplexes provides insights into DNA repair
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
Plugged into the Ku-DNA hub: The NHEJ network
Frit, P., Ropars, V., Modesti, M., Charbonnier, J., & Calsou, P. (2019) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2019.03.001 · Cited by 81 · see citing works
Guggenheim, E. R., Dong, X., Zhang, C. X., Chang, P. V., & Lippard, S. J. (2008) · ChemBioChem · doi:10.1002/cbic.200800471 · Cited by 70 · see citing works
Sears, C. R., & Turchi, J. J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.344911 · Cited by 65 · see citing works
Biologic Activity of a Dinuclear Pd(II)–Spermine Complex Toward Human Breast Cancer
Fiuza, S. M., Holy, J. M., de Carvalho, L. A. E. B., & Marques, M. P. M. (2011) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2011.01081.x · Cited by 51 · see citing works
Andrews, B. J., Lehman, J. A., & Turchi, J. J. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m512787200 · Cited by 49 · see citing works
Discovery and development of novel DNA-PK inhibitors by targeting the unique Ku–DNA interaction
Gavande, N. S., VanderVere-Carozza, P. S., Pawelczak, K. S., Mendoza-Munoz, P. L., Vernon, T. L., Hanakahi, L. A., Summerlin, M., Dynlacht, J. R., Farmer, A. H., Sears, C. R., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa934 · Cited by 46 · see citing works
DNA-dependent conformational changes in the Ku heterodimer
Lehman, J. A., Hoelz, D. J., & Turchi, J. J. (2008) · Biochemistry · doi:10.1021/bi702284c · Cited by 43 · see citing works
Jovanović, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj504 · Cited by 39 · see citing works
Diggle, C. P. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki528 · Cited by 39 · see citing works
Pawelczak, K. S., & Turchi, J. J. (2010) · DNA repair · doi:10.1016/j.dnarep.2010.03.002 · Cited by 38 · see citing works
Coordination of DNA-PK activation and nuclease processing of DNA termini in NHEJ
Pawelczak, K. S., Bennett, S. M., & Turchi, J. J. (2011) · Antioxidants & Redox Signaling · doi:10.1089/ars.2010.3368 · Cited by 33 · see citing works
Pawelczak, K. S., & Turchi, J. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn344 · Cited by 33 · see citing works
Self-citationTian, X., Chen, G., Xing, H., Weng, D., Guo, Y., & Ma, D. (2007) · Oncology Reports · doi:10.3892/or.18.4.927 · Cited by 32 · see citing works
Radhakrishnan, S. K., & Lees‐Miller, S. P. (2017) · DNA repair · doi:10.1016/j.dnarep.2017.06.001 · Cited by 27 · see citing works
Kelm, J. M., Samarbakhsh, A., Pillai, A., VanderVere-Carozza, P. S., Aruri, H., Pandey, D. S., Pawelczak, K. S., Turchi, J. J., & Gavande, N. S. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.850883 · Cited by 26 · see citing works
Activation of DNA-PK by hairpinned DNA ends reveals a stepwise mechanism of kinase activation
Meek, K. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa614 · Cited by 25 · see citing works
Activities of DNA-PK and Ku86, but not Ku70, may predict sensitivity to cisplatin in human gliomas
Shao, C.-J., Fu, J., Shi, H.-L., Mu, Y., & Chen, Z.-P. (2008) · Journal of Neuro-Oncology · doi:10.1007/s11060-008-9592-7 · Cited by 23 · see citing works
Woods, D. S., Sears, C. R., & Turchi, J. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127321 · Cited by 22 · see citing works
Nishida, Y., Mizutani, N., Inoue, M., Omori, Y., Tamiya‐Koizumi, K., Takagi, A., Kojima, T., Suzuki, M., Nozawa, Y., Minami, Y., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.02.004 · Cited by 22 · see citing works
Modeling non-homologous end joining
Li, Y., & Cucinotta, F. A. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.05.015 · Cited by 18 · see citing works
Yuan, Y., Britton, S., Delteil, C., Coates, J., Jackson, S. P., Barboule, N., Frit, P., & Calsou, P. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv894 · Cited by 17 · see citing works
“An End to a Means”: How DNA-End Structure Shapes the Double-Strand Break Repair Process
Serrano-Benítez, A., Cortés‐Ledesma, F., & Ruiz, J. F. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2019.00153 · Cited by 17 · see citing works
DNA-dependent protein kinase: Epigenetic alterations and the role in genomic stability of cancer
Vazhappilly, C. G., Ansari, S. A., Chelakkot, V. S., Chelakkot, A. L., Chelakkot, C., Menon, V., Ramadan, W. S. H., Radhakrishnan, E. K., El‐Awady, R., Mantso, T., et al. (2018) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2018.06.001 · Cited by 16 · see citing works
Resolution of complex ends by Nonhomologous end joining - better to be lucky than good?
Strande, N. T., Waters, C. A., & Ramsden, D. A. (2012) · Genome Integrity · doi:10.1186/2041-9414-3-10 · Cited by 13 · see citing works
Bennett, S. M., Woods, D. S., Pawelczak, K. S., & Turchi, J. J. (2012) · PubMed Central · Cited by 11 · see citing works
Integration of DNA damage and repair with murine double-minute 2 (Mdm2) in tumorigenesis
Lehman, J., & Mayo, L. (2012) · International Journal of Molecular Sciences · doi:10.3390/ijms131216373 · Cited by 9 · see citing works
D’Aiuto, L., Marco, R. D., Nwanegbo, E. C., Rizzo, A., Chaillet, J. R., Montecalvo, A., Lotze, M. T., & Gambotto, A. A. (2006) · DNA and Cell Biology · doi:10.1089/dna.2006.25.171 · Cited by 9 · see citing works
Merlin, J. P. J., Rajan, S. S., & Abrahamse, H. (2025) · Cancer Medicine · doi:10.1002/cam4.71032 · Cited by 7 · see citing works
Impact of Optimized Ku–DNA Binding Inhibitors on the Cellular and In Vivo DNA Damage Response
Mendoza-Munoz, P. L., Kushwaha, N. D., Chauhan, D., Gacem, K. B. A., Garrett, J., Dynlacht, J. R., Charbonnier, J., Gavande, N. S., & Turchi, J. J. (2024) · Cancers · doi:10.3390/cancers16193286 · Cited by 4 · see citing works
Chen, C., & Bridge, E. (2021) · Virology · doi:10.1016/j.virol.2021.10.011 · Cited by 4 · see citing works
ERCC6L2 ensures repair fidelity for staggered-end DNA double-strand breaks
Aird, E. J., Serrano-Benítez, A., Siegner, S. M., Cannavò, E., Belotserkovskaya, R., Gueorguieva, N., Fielden, J., Cullot, G., Ammann, S., Bader, A. S., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69843-w · Cited by 3 · see citing works
Qiu, Y., Lin, X., Mladenov, E., Mladenova, V., Thomale, J., Sak, A., Wang, Y., Deng, Y., Gkika, E., Stuschke, M., et al. (2026) · Molecular Oncology · doi:10.1002/1878-0261.70240 · Cited by 2 · see citing works
Woods, D. S. (2014) · IUScholarWorks (Indiana University) · doi:10.7912/c2/1851
Kushwaha, N. D., VanderVere-Carozza, P. S., Vernon, T. L., Mendoza-Munoz, P. L., Gaddameedi, J. D., Gacem, K. B. A., Engel, J., Charbonnier, J., Gavande, N. S., & Turchi, J. J. (2025) · RSC Medicinal Chemistry · doi:10.1039/d5md00263j
- Authors
- Pawelczak, K. S.
- Affiliations
- Wright State University (US)
- Corresponding author
- Pawelczak, K. S.
- ORCID
- Pawelczak, K. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-01-07
- Volume
- 33
- Issue
- 1
- Pages
- 152-161
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC546145
- OpenAlex
- W2052349609
- Cited by
- 42
- References
- 27
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 1 · 2022: 1 · 2021: 2 · 2020: 3 · 2019: 1 · 2018: 1 · 2017: 2 · 2015: 2 · 2014: 2 · 2013: 1 · 2012: 5
- FWCI
- 1.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- other-oa
- Locations
- Nucleic Acids Research (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- 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 › Oncology › Metal complexes synthesis and properties
- Keywords
- DNA-PKcs, Ku heterodimer, non-homologous end joining, DNA double-strand breaks, kinase activation, sequence bias, cisplatin-DNA adducts, DNA structure
- MeSH terms
- Base Sequence, Cisplatin, DNA, DNA-Binding Proteins, Enzyme Activation, Purine Nucleotides, Pyrimidine Nucleotides, Protein Serine-Threonine Kinases, DNA Adducts, DNA-Activated Protein Kinase
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
