Formation of Complex Spatial Structure of DNA in the Process of ab initio Synthesis

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Products with a complex spatial organization are formed during the ab initio synthesis under the action of Bst DNA polymerase, large fragment. Using the analysis of AFM images of the products obtained with the addition of a minimal amount of the nicking endonuclease Nt. BspD6I during this synthesis, it became possible to describe the structures formed as a result of this synthesis and suggest that their formation occurs by the mechanism of replication-dependent recombination.

About the authors

N. V Zyrina

Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences; Institute for Biological Instrumentation, Russian Academy of Sciences

Pushchino, Russia

O. M Selivanova

Institute of Protein Research, Russian Academy of Sciences

Pushchino, Russia

E. V Shevchenko

The Saint Petersburg State University Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics

Saint Petersburg, Russia

V. N Antipova

Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences

Email: valery_a@rambler.ru
Pushchino, Russia

References

  1. Zyrina N. V., Antipova V. N., and Zheleznaya L. A. Ab initio synthesis by DNA polymerases. FEMS Microbiol. Lett., 351 (1), 1 (2014). doi: 10.1111/1574-6968.12326
  2. Zyrina N. V., Zheleznaya L. A., Dvoretsky E. V., VasilievV. D., Chernov A., and Matvienko N. I. N.BspD6I DNA nickase strongly stimulates template-independent synthesis of non-palindromic repetitive DNA by Bst DNA polymerase. Biol. Chem., 388 (4), 367-372 (2007). doi: 10.1515/BC.2007.043
  3. Cheng D. W. and Calderón-Urrea A. Nontemplate polymerization of free nucleotides into genetic elements by thermophilic DNA polymerase in vitro. Nucleosides Nucleotides Nucl. Acids, 30 (11), 979-990 (2011). doi: 10.1080/15257770.2011.628637
  4. Antipova V. N., Reveguk Z. V., Kraynyukov E. S., and Zyrina N. V. Structure of DNA obtained during the ab initio synthesis by Bst DNA polymerase in the presence of the nicking endonuclease from Bacillus stearothermophilus (Nt.BstNBI). J. Biomol. Struct. Dyn., 37 (13), 3314-3321 (2019). doi: 10.1080/07391102.2018.1515662
  5. Andersen E. S., Contera S. A., Knudsen B., Damgaard C. K., Besenbacher F., and Kjems J. Role of the trans-activation response element in dimerization of HIV-1 RNA. J. Biol. Chem., 279 (21), 22243 (2004). doi: 10.1074/jbc.M314326200
  6. Ma H., Jia X., Zhang K., and Su Z. Cryo-EM advances in RNA structure determination. Signal. Transduct. Target Ther., 7 (1), 58 (2022). doi: 10.1038/s41392-022-00916-0
  7. Pierce P. G. and Hancock R. L. Electron microscopy of negatively stained tRNA. Nature, 241, 529-530 (1973). doi: 10.1038/241529a0
  8. Meyer J. Electron microscopy of viral RNA (Springer-Verlag, Berlin-Heidelberg, 1981)
  9. Железная Л. А., Качалова Г. С., Артюх Р. И., Юнусова А. К., Перевязова Т. А. и Матвиенко Н. И. Никующие эндонуклеазы. Успехи биол. химии, 49, 107-128 (2009)
  10. Klinov D. V., Lagutina I. V., Prokhorov V. V., Neretina T., Khil P. P., Lebedev Y. B., Cherny D. I., Demin V. V., and Sverdlov E. D. High resolution mapping DNAs by R-loop atomic force microscopy. Nucl. Acids Res., 26 (20), 46034610 (1998). doi: 10.1093/nar/26.20.4603
  11. Carrasco-Salas Y., Malapert A., Sulthana S., Molcrette B., Chazot-Franguiadakis L., Bernard P., Ché-din F., Faivre-Moskalenko C., and Vanoosthuyse V. The extruded non-template strand determines the architecture of R-loops. Nucl. Acids Res., 47 (13), 6783-6795 (2019). doi: 10.1093/nar/gkz341
  12. Backert S. R-loop-dependent rolling-circle replication and a new model for DNA concatemer resolution by mitochondrial plasmid mp1. EMBO J., 21 (12), 3128-3136 (2002). doi: 10.1093/emboj/cdf311
  13. Greider C. W. Telomeres do D-loop-T-loop. Cell, 97 (4), 419-422 (1999). doi: 10.1016/s0092-8674(00)80750-3
  14. Axford M. M., Wang Y. H., Nakamori M., Zannis-Hadjopoulos M., Thornton C. A., and Pearson C. E. Detection of slipped-DNAs at the trinucleotide repeats of the myotonic dystrophy type I disease locus in patient tissues. PLoS Genet., 9 (12), e1003866 (2013). doi: 10.1371/journal.pgen.1003866
  15. Sinden R. R., Potaman V. N., Oussatcheva E. A., Pearson C. E., Lyubchenko Y. L., and Shlyakhtenko L. S. Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J. Biosci., 27, 53-65 (2002). doi: 10.1007/BF02703683
  16. Zhang S., Tang L., Zhang J., Sun W., Liu D., Chen J., Hu B., and Huang Z. Single-atom-directed inhibition of de Novo DNA synthesis in isothermal amplifications. Anal. Chem., 94 (45), 15763-15771 (2022). doi: 10.1021/acs.analchem.2c03489
  17. Ogata N. and Miura T. Genetic information 'created' by archaebacterial DNA polymerase. Biochem. J., 324 (Pt 2), 667-671 (1997). doi: 10.1042/bj3240667
  18. Ogata N. and Morino H. Elongation of repetitive DNA by DNA polymerase from a hyperthermophilic bacterium Thermus thermophilus. Nucl. Acids Res., 28 (20), 39994004 (2000). doi: 10.1093/nar/28.20.3999
  19. Mosig G. Recombination and recombination-dependent DNA replication in bacteriophage T4. Annu. Rev. Genetics, 32, 379-413 (1998). doi: 10.1146/annurev.gen-et.32.1.379
  20. Cheng N., Lo Y. S., Ansari M. I., Ho K. C., Jeng S. T., Lin N. S., and Dai H. Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination. New Phytologist, 213 (2), 751-763 (2017). doi: 10.1111/nph.14158
  21. Severini A., Scraba D. G., and Tyrrell D. L. Branched structures in the intracellular DNA of herpes simplex virus type 1. J. Virology, 70 (5), 3169-3175 (1996). doi: 10.1128/JVI.70.5.3169-3175.1996
  22. Tomaska L., Nosek J., Kar A., Willcox S., and Griffith J. D. A new view of the T-loop junction: implications for self-primed telomere extension, expansion of disease-related nucleotide repeat blocks, and telomere evolution. Front. Genetics, 10, 792 (2019). doi: 10.3389/fgene.2019.00792
  23. Nabetani A. and Ishikawa F. Unusual telomeric DNAs in human telomerase-negative immortalized cells. Mol. Cell. Biol., 29 (3), 703-713 (2009). doi: 10.1128/MCB.00603-08
  24. Wang G., Ding X., Hu J., Wu W., Sun J., and Mu Y. Unusual isothermal multimerization and amplification by the strand-displacing DNA polymerases with reverse transcription activities. Sci. Rep., 7 (1), 13928 (2017). doi: 10.1038/s41598-017-13324-0
  25. Tsai C. H., Chen J., and Szostak J. W. Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template. Proc. Nat. Acad. Sci. USA, 104 (37), 14598-14603 (2007). doi: 10.1073/pnas.0704211104
  26. Oscorbin I. and Filipenko M. Bst polymerase - a humble relative of Taq polymerase. Comput. Struct. Biotechnol. J., 21, 4519-4535 (2023). doi: 10.1016/j.csbj.2023.09.008
  27. Tomaska L., Nosek J., Kar A., Willcox S. and Griffith J. D. A new view of the t-loop junction: implications for self-primed telomere extension, expansion of disease-related nucleotide repeat blocks, and telomere evolution. Front. Genetics, 10, 792 (2019). doi: 10.3389/fgene.2019.00792
  28. Hou K., Yu Y., Li D., Zhang Y., Zhang K., Tong J., Yang K., and Jia S. Alternative lengthening of telomeres and mediated telomere synthesis. Cancers, 14 (9), 2194 (2022). doi: 10.3390/cancers14092194
  29. West S. C. Processing of recombination intermediates by the RuvABC proteins. Annu. Rev. Genetics, 31, 213-244 (1997). doi: 10.1146/annurev.genet.31.1.213
  30. Liang X., Jensen, K., and Frank-Kamenetskii M. D. Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic restriction endonuclease. Biochemistry, 43 (42), 13459-13466 (2004). doi: 10.1021/bi0489614

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2024 Russian Academy of Sciences