Biomics

DNA-dependent DNA polymerases are multifunctional enzymes. In addition to their main purpose of building a new DNA chain complementary to the template, they act as exonucleases, characterized by multidirectional 3’→5’-editing and 5’→3’-repairing activities, for which the corresponding domains of this large protein are responsible. The domains responsible for exonuclease activities are located at the N-terminus of the protein, whereas the nucleotidyltransferase domain is located at the C-terminus and this topology of their organization is practically the same for all these enzymes. In addition, some DNA polymerases have strand-displacement activity instead of repairing activity. DNA polymerases are also capable to catalyze pyrophosphorolysis. The DNA polymerases found in different organisms form seven families, of which the thermostable enzymes of Eubacteria from the A family and archaeal enzymes from the B family are used in PCR. Archaeal DNA polymerases carry editing activity, providing higher fidelity during amplification. Some genetically engineered DNA polymerases lack exonuclease activities.

DNA polymerase, family of DNA polymerases, polymerase domain, 5’→3’-exonuclease domain, 3’→5’ exonuclease domain, repairing activity, editing activity, pyrophosphorolysis

1. 1. Bessman MJ, Lehman IR, Simms ES et al. Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction. J Biol Chem. 1958. 233(1). 171-177. doi: 10.1016/S0021-9258(19)68049-X
   2. Braithwaite DK, Ito J. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 1993. 21(4). 787-802. doi: 10.1093/nar/21.4.787
   3. Bollum FJ. Calf thymus polymerase. J Biol Chem. 1960. 235(8). 2399-2403. doi: 10.1016/S0021-9258(18)64634-4
   4. Burgers PM, Koonin EV, Bruford E et al. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem. 2001. 276(47). 43487-43490. doi: 10.1074/jbc.R100056200
   5. Case BC, Hingorani MM. Polymerase. In: Reference Module in Life Sciences, Elsevier, 2017. doi: 10.1016/B978-0-12-809633-8.06928-4
   6. Delarue M, Poch O, Tordo N et al. An attempt to unify the structure of polymerases. Protein Eng. 1990. 3(6). 461-467. doi: 10.1093/protein/3.6.461
   7. Garafutdinov RR, Nikonorov YuM, Sakhabutdinova AR et al. Enzymatic synthesis of oligonucleotides. Biomics. 2025. 17(4). 337-351. doi: 10.31301/2221-6197.bmcs.2025-30 (In Russian)
   8. Ito J, Braithwaite DK. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res. 1991. 19(15). 4045-4057. doi: 10.1093/nar/19.15.4045
   9. Jain R, Aggarwal AK, Rechkoblit O. Eukaryotic DNA polymerases. Curr Opin Struct Biol. 53. 77-87. doi: 10.1016/j.sbi.2018.06.003
   10. Jayasinghe MI, Patel KJ, Jackman JE. Thg1 family 3`-5` RNA polymerases as tools for targeted RNA synthesis. RNA. 2024. 30(10). 1315-1327. doi: 10.1261/rna.080156.124
   11. Joyce CM, Grindley ND. Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli. Proc Natl Acad Sci USA. 1983. 80(7). 1830-1834. doi: 10.1073/pnas.80.7.1830
   12. Joyce CM, Kelley WS, Grindley ND. Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. J Biol Chem. 1982. 257(4). 1958-1964. doi: 10.1016/S0021-9258(19)68132-9
   13. Klenow H, Overgaard-Hansen K. Proteolytic cleavage of DNA polymerase from Escherichia coli B into an exonuclease unit and a polymerase unit. FEBS Lett. 1970. 6(1). 25-27. doi: 10.1016/0014-5793(70)80032-1
   14. Kornberg A, Lehman LR, Simms ES. Polydesoxyribonucleotide synthesis by enzymes from Escherichia coli. Federation Proceedings. 15(1). 291-292.
   15. Kuznetsova AA, Fedorova OS, Kuznetsov NA. Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci. 2022. 23(12). 6373. doi: 10.3390/ijms23126373
   16. Lehman IR, Bessman MJ, Simms ES et al. A. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem. 1958. 233(1). 163-170. doi: 10.1016/S0021-9258(19)68048-8
   17. Nakamura A, Nemoto T, Heinemann IU et al. Structural basis of reverse nucleotide polymerization. Proc Natl Acad Sci USA. 2013. 110(52). 20970-20975. doi: 10.1073/pnas.1321312111
   18. Ollis DL, Brick P, Hamlin R et al. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature. 1985. 313(6005). 762-726. doi: 10.1038/313762a0