- PII
- S30345294S0320972525080118-1
- DOI
- 10.7868/S3034529425080118
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 90 / Issue number 8
- Pages
- 1219-1228
- Abstract
- DNA damage leads to distortion of the B-form structure of its double helix. Recognition of such distortion by DNA repair proteins is an important step in initiating this process. The nucleosome structure imposes limitations on the mobility and plasticity of DNA geometry in its composition. When studying the interactions of repair proteins with DNA in the composition of the nucleosome, the main question lies in realizing the DNA structure characteristic of the damage itself in a particular context. Additionally, the DNA duplex in the nucleosome has a regular contact profile with histones corresponding to the pitch of the DNA helix. Changes in this profile allow us to determine changes in the DNA structure. This profile correlates with the availability of relevant nucleotides for interacting with DNA-binding proteins. Using the footprinting method, we showed that the presence of an apurine/apiridine site within the second-third turn of the spiral from the 5'-end in the nucleosomal DNA did not have a significant effect on the profile of DNA-histone contacts.
- Keywords
- нуклеосома апуриновый/апиримидиновый сайт футпринтинг
- Date of publication
- 04.08.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 93
References
- 1. Chen, J., Dupradeau, F.-Y., Case, D. A., Turner, C. J., and Stubbe, J. (2008) DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics, Nucleic Acids Res., 36, 253-262, https://doi.org/10.1093/nar/gkm622.
- 2. Wilson, D. M. 3rd. (2005) Ape1 abasic endonuclease activity is regulated by magnesium and potassium concentrations and is robust on alternative DNA structures, J. Mol. Biol., 345, 1003-1014, https://doi.org/10.1016/j.jmb.2004.11.028.
- 3. Fan, J., Matsumoto, Y., and Wilson, D. M. 3rd. (2006) Nucleotide sequence and DNA secondary structure, as well as replication protein A, modulate the single-stranded abasic endonuclease activity of APE1, J. Biol. Chem., 281, 3889-3898, https://doi.org/10.1074/jbc.M511004200.
- 4. Hinz, J. M. (2014) Impact of abasic site orientation within nucleosomes on human APE1 endonuclease activity, Mutat. Res., 766-767, 19-24, https://doi.org/10.1016/j.mrfmmm.2014.05.008.
- 5. Olmon, E. D., and Delaney, S. (2017) Differential ability of five DNA glycosylases to recognize and repair damage on nucleosomal DNA, ACS Chem. Biol., 12, 692-701, https://doi.org/10.1021/acschembio.6b00921.
- 6. Beard, B. C., Wilson, S. H., and Smerdon, M. J. (2003) Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes, Proc. Natl. Acad. Sci. USA, 100, 7465-7470, https://doi.org/10.1073/pnas.1330328100.
- 7. Osakabe, A., Arimura, Y., Matsumoto, S., Horikoshi, N., Sugasawa, K., and Kurumizaka, H. (2017) Polymorphism of apyrimidinic DNA structures in the nucleosome, Sci. Rep., 7, 41783, https://doi.org/10.1038/srep41783.
- 8. Peterson, C. L., and Hansen, J. C. (2008) Chicken erythrocyte histone octamer preparation, CSH Protocols, 2008, pdb.prot5112, https://doi.org/10.1101/pdb.prot5112.
- 9. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, Cold Spring Harbor Laboratory Press, N.Y.
- 10. Luger, K., Rechsteiner, T. J., and Richmond, T. J. (1999) Expression and purification of recombinant histones and nucleosome reconstitution, Methods Mol. Biol., 119, 1-16, https://doi.org/10.1385/1-59259-681-9:1.
- 11. Lowary, P. T., and Widom, J. (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning, J. Mol. Biol., 276, 19-42, https://doi.org/10.1006/jmbi.1997.1494.
- 12. Armeev, G. A., Kniazeva, A. S., Komarova, G. A., Kirpichnikov, M. P., and Shaytan, A. K. (2021) Histone dynamics mediate DNA unwrapping and sliding in nucleosomes, Nat. Commun., 12, 2387, https://doi.org/10.1038/s41467-021-22636-9.
- 13. Chen, Z., Gabizon, R., Brown, A. I., Lee, A., Song, A., Díaz-Celis, C., Kaplan, C. D., Koslover, E. F., Yao, T., Bustamante, C. (2019) High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier, Elife, 8, e48281, https://doi.org/10.7554/eLife.48281.
- 14. Balasubramanian, B., Pogozelski, W. K., and Tullius, T. D. (1998) DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone, Proc. Natl. Acad. Sci. USA, 95, 9738-9743, https://doi.org/10.1073/pnas.95.17.9738.
- 15. Andreeva, N. A., Maluchenko, N. V., Sivkina, A. L., Chertkov, O. V., Valieva, M. E., Kotova, E. Y., Kirpichnikov, M. P., Studitsky, V. M., and Feofanov, A. V. (2022) Na+ and K+ ions differently affect nucleosome structure, stability, and interactions with proteins, Microsc. Microanal., 28, 243-253, https://doi.org/10.1017/S1431927621013751.
- 16. Weaver, N. M., Hoitsma, N. M., Spencer, J. J., Gakhar, L., Schnicker, N. J., and Freudenthal, B. D. (2022) Structural basis for APE1 processing DNA damage in the nucleosome, Nat. Commun., 13, 5390, https://doi.org/10.1038/s41467-022-33057-7.
- 17. Carey, D. C., and Strauss, P. R. (1999) Human apurinic/apyrimidinic endonuclease is processive, Biochemistry, 38, 16553-16560, https://doi.org/10.1021/bi9907429.
- 18. Hinz, J. M., Rodriguez, Y., and Smerdon, M. J. (2010) Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme, Proc. Natl. Acad. Sci. USA, 107, 4646-4651, https://doi.org/10.1073/pnas.0914443107.
