Biomics

DNA polymerases are a key component of DNA synthesis reactions. For their functioning, the presence of divalent metal cations in the reaction mixture is required. The most typical cofactor is the Mg2+ ion; however, there are data on the manifestation of polymerase activity by some DNA polymerases in the presence of other cations. Previously, such data were obtained mainly for DNA polymerases that do not have stranddisplacement activity. In this study, quaternary complexes containing DNA, triphosphate, Ca2+, Cd2+, Co2+, Cu2+, Mg2+, Mn2+, Ni2+, or Zn2+ cations in various combinations, and KlenTaq polymerase, which is able to displace the old strand during the synthesis of a new one, were studied using molecular docking. The energy parameters of the complexes, as well as the positions and types of chemical bonds, were determined. It was found that the maximum number of ionic bonds is formed in the presence of cation combinations Mg2+/Cd2+ and Mg2+/Mg2+ ions.

nucleic acids, amplification, DNA polymerases, cofactors, molecular docking, molecular modeling

1. Bikbulatova S.M., Chemeris D.A., Nikonorov Yu.M., Mashkov O.I., Garafutdinov R.R., Chemeris A.V., Vakhitov V.A. Methods for
detection of real-time polymerase chain reaction results. Vestn. Bashkir State University. 2012. V. 17. No. 1. S. 59-67. (In Russian)

2. Broeders S.R., De Keersmaecker S.C., Roosens N.H. How to deal with the upcoming challenges in GMO detection in food and feed. J. Biomed. Biotechnol. 2012. 402418. https://doi.org/10.1155/2012/402418

3. Burtis C.A., Ashwood E.R., Bruns D.E. 2013. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. 5th ed. St. Louis: Saunders Elsevier.

4. Chemeris A.V., Aminev F.G., Garafutdinov R.R., Anisimov V.A., Sagitov A.M., Khusnutdinova E.K., Sakhabutdinova A.R., Chemeris D.A., Mikhailenko K.I. DNA forensics. M.: Nauka, 2022. 466 p. (In Russian)

5. Chemeris A.V., Chemeris D.A., Magdanov E.G., Garafutdinov R.R., Nagaev N.R., Vakhitov V.A. Causes of false-negative PCR and prevention of some of them. Biomics. 2012. V. 4. No. 1. S. 31-47. (In Russian)

6. Chemeris A.V., Magdanov E.G., Garafutdinov R.R., Vakhitov V.A. How to exclude the appearance of false-positive results during the polymerase chain reaction? Vestn. biotechnol. fiz.-chem. biol. 2012. V. 8. No. 3. S. 34-45. (In Russian)

7. Chemeris D.A., Magdanov E.G., Mashkov O.I., Garafutdinov R.R., Chemeris A.V. Delayed (hotstart) PCR. Biomics. 2011. V. 2. No. 1. S. 1-8. (In Russian)

8. Compton J. Nucleic acid sequence-based amplification. Nature. 1991. V. 350(6313). P. 91-92. https://doi.org/10.1038/350091a0

9. Fire A., Xu S.Q. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci USA. 1995. V. 92(10). P. 4641-4645. https://doi.org/10.1073/pnas.92.10.4641 

10. Friesner R.A., R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, D.T. Mainz, Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes. J. Med. Chem. 2006. V. 49. P. 6177-6196. https://doi.org/10.1021/jm051256o

11. Garafutdinov R.R., Galimova A.A., Sakhabutdinova A.R. Polymerase Chain Reaction With Nearby Primers. Anal. Biochem. 2017. V. 518. P. 126-133. https://doi.org/10.1016/j.ab.2016.11.017

12. Garafutdinov R.R., Galimova A.A., Sakhabutdinova A.R., Vakhitov V.A., Chemeris A.V. PCR amplification of DNA with abutting
primers. Mol. biol. 2015. V. 49. No. 4. P. 628. https://doi.org/10.7868/S0026898415040059

13. Garafutdinov R.R., Gilvanov A.R., Kupova O.Y., Sakhabutdinova A.R. Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase. Int. J. Biol. Macromol. 2020. V. 161. P. 1447-1455. https://doi.org/10.1016/j.ijbiomac.2020.08.028

14. Garafutdinov R.R., Gilvanov A.R., Sakhabutdinova A.R. The influence of reaction conditions on DNA multimerization during isothermal amplification with Bst DNA polymerase. Appl. Biochem. Biotechnol. 2020. V. 190. P. 758-771. https://doi.org/10.1007/s12010-019-03127-6

15. Garafutdinov R.R., Kupova O.Yu., Gilvanov A.R., Sakhabutdinova A.R. Data on molecular docking simulations of quaternary complexes 'Bst exopolymerase-DNA-dCTP-metal cations'. Data-inBrief. 2020. V. 33, 106549. https://doi.org/10.1016/j.dib.2020.106549

16. Garafutdinov R.R., Sakhabutdinova A.R., Gilvanov A.R., Chemeris A.V. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. Russ. J. Bioorg. Chem. 2021. V. 47(6). P. 1172-1189. https://doi.org/10.1134/S1068162021060078

17. Garafutdinov R.R., Sakhabutdinova A.R., Kupryushkin M.S., Pyshnyi D.V. Prevention of DNA multimerization during isothermal
amplification with Bst exo- DNA polymerase. Biochimie. 2020. V. 168. P. 259-267. https://doi.org/10.1016/j.biochi.2019.11.013

18. Khanova L.I., Garafutdinov R.R., Sakhabutdinova A.R., Chemeris A.V. The influence of DNA templates composition on nonspecific (ab initio) DNA synthesis. Biomics. 2022. V.14(1). P. 359-367. https://doi.org/10.31301/2221-6197.bmcs.2022-38 (In Russian)

19. Myers T.W., Gerald D.H. Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry. 1991. V. 30. P. 7661-7666. https://doi.org/10.1021/bi00245a001

20. Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., Amino N., Hase T. Loopmediated isothermal amplification of DNA. Nucleic Acids Res. 2000. V. 28(12). E63. https://doi.org/10.1093/nar/28.12.e63

21. Ralec C., Henry E., Lemor M., Killelea T., Henneke G. Calcium-driven DNA synthesis by a high-fidelity DNA polymerase. Nucleic Acids Res. 2017. V. 45. P. 12425-12440. https://doi.org/10.1093/nar/gkx927

22. Saiki R.K., Scharf S., Faloona F., Mullis K.B., Horn G.T., Erlich H.A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985. V. 230. P. 1350-1354. https://doi.org/10.1126/science.2999980

23. Sakhabutdinova A.R., Kamalov M.I., Salakhieva D.V., Mavzyutov A.R., Garafutdinov R.R. Inhibition of nonspecific polymerase activity using Poly(Aspartic) acid as a model anionic polyelectrolyte. Anal. Biochem. 2021. V. 628. 114267. https://doi.org/10.1016/j.ab.2021.114267

24. Sakhabutdinova A.R., Mirsaeva L.R., Oscorbin I.P., Filipenko M.L., Garafutdinov R.R. Elimination of DNA Multimerization Arising from Isothermal Amplification in the Presence of Bst Exo- DNA Polymerase. Rus. J. Bioorg. Chem. 2020. V. 46. P. 52-59. https://doi.org/10.1134/s1068162020010082

25. Sastry G.M., Adzhigirey M., Day T., Annabhimoju R., Sherman W. Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aid. Mol. Des. 2013. V. 27. P. 221-234. https://doi.org/10.1007/s10822-013-9644-8

26. Steitz T.A. A mechanism for all polymerases. Nature. 1998. V. 391. P. 231-232. https://doi.org/10.1038/34542.

27. Tsai M.-D. Catalytic mechanism of DNA polymerases - Two metal ions or three? Protein Sci. 2019. V. 28. P. 288-291. https://doi.org/10.1002/pro.3542 

28. Vashishtha A.K., Konigsberg W.H. Effect of different divalent cations on the kinetics and fidelity of Bacillus stearothermophilus DNA polymerase. Biochemistry. 2018. V. 55. P. 2661-2670. https://doi.org/10.3934/biophy.2018.2.125

29. Vashishtha A.K., Wang J., Konigsberg W.H. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. J. Biol. Chem. 2016. V. 291. P. 20869-20875. https://doi.org/10.1074/jbc.R116.742494

30. Walter N.G., Strunk G. Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer. Proc. Natl. Acad. Sci. USA. 1994. V. 91(17). P. 7937-7941. https://doi.org/10.1073/pnas.91.17.7937

31. Yang W., Weng P.J., Gao Y. A new paradigm of DNA synthesis: three-metal-ion catalysis. Cell Biosci. 2016. V. 6. P. 51. https://doi.org/10.1186/s13578-016-0118-2

32. Zyrina N.V., Antipova V.N., Zheleznaya L.A. Ab initio synthesis by DNA polymerases. FEMS Microbiol. Lett. 2014. V. 351. P. 1-6. https://doi.org/10.1111/1574-6968.12326