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Journal articles on the topic 'DNA-Directed DNA Polymerase/genetics'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Santos, M. E., and J. W. Drake. "Rates of spontaneous mutation in bacteriophage T4 are independent of host fidelity determinants." Genetics 138, no. 3 (1994): 553–64. http://dx.doi.org/10.1093/genetics/138.3.553.

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Abstract Bacteriophage T4 encodes most of the genes whose products are required for its DNA metabolism, and host (Escherichia coli) genes can only infrequently complement mutationally inactivated T4 genes. We screened the following host mutator mutations for effects on spontaneous mutation rates in T4: mutT (destruction of aberrant dGTPs), polA, polB and polC (DNA polymerases), dnaQ (exonucleolytic proofreading), mutH, mutS, mutL and uvrD (methyl-directed DNA mismatch repair), mutM and mutY (excision repair of oxygen-damaged DNA), mutA (function unknown), and topB and osmZ (affecting DNA topol

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2

CHANG, GWONG-JEN J., BARBARA J. B. JOHNSON, and DENNIS W. TRENT. "Site-Specific Oligonucleotide-Directed Mutagenesis Using T4 DNA Polymerase." DNA 7, no. 3 (1988): 211–17. http://dx.doi.org/10.1089/dna.1988.7.211.

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3

Wright, G. E. "Nucleotide probes of DNA polymerases." Acta Biochimica Polonica 43, no. 1 (1996): 115–24. http://dx.doi.org/10.18388/abp.1996_4522.

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The modified nucleotides, N2-(p-n-butylphenyl)dGTP and 2-(p-n-butylanilino) dATP and related compounds have been developed as inhibitor-probes of B family DNA polymerases. Synthetic approaches to these compounds are summarized. The nucleotides are potent, non-substrate inhibitors of DNA polymerase a. In contrast, they inhibit other members of the family with less potency but act as substrates for these enzymes. Modelling of the inhibitor: enzyme binding mechanism has been done based on the known structure of E. coli DNA polymerase I, and site-directed mutagenesis experiments to evaluate this m

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4

Hadjimarcou, Michalis I., Robert J. Kokoska, Thomas D. Petes та Linda J. Reha-Krantz. "Identification of a Mutant DNA Polymerase δ in Saccharomyces cerevisiae With an Antimutator Phenotype for Frameshift Mutations". Genetics 158, № 1 (2001): 177–86. http://dx.doi.org/10.1093/genetics/158.1.177.

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Abstract We propose that a β-turn-β structure, which plays a critical role in exonucleolytic proofreading in the bacteriophage T4 DNA polymerase, is also present in the Saccharomyces cerevisiae DNA pol δ. Site-directed mutagenesis was used to test this proposal by introducing a mutation into the yeast POL3 gene in the region that encodes the putative β-turn-β structure. The mutant DNA pol δ has a serine substitution in place of glycine at position 447. DNA replication fidelity of the G447S-DNA pol δ was determined in vivo by using reversion and forward assays. An antimutator phenotype for fram

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5

Adereth, Yair, Kristen J. Champion, Tien Hsu, and Vincent Dammai. "Site-directed mutagenesis using Pfu DNA polymerase and T4 DNA ligase." BioTechniques 38, no. 6 (2005): 864–68. http://dx.doi.org/10.2144/05386bm03.

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6

Fijalkowska, I. J., and R. M. Schaaper. "Antimutator mutations in the alpha subunit of Escherichia coli DNA polymerase III: identification of the responsible mutations and alignment with other DNA polymerases." Genetics 134, no. 4 (1993): 1039–44. http://dx.doi.org/10.1093/genetics/134.4.1039.

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Abstract The dnaE gene of Escherichia coli encodes the DNA polymerase (alpha subunit) of the main replicative enzyme, DNA polymerase III holoenzyme. We have previously identified this gene as the site of a series of seven antimutator mutations that specifically decrease the level of DNA replication errors. Here we report the nucleotide sequence changes in each of the different antimutator dnaE alleles. For each a single, but different, amino acid substitution was found among the 1,160 amino acids of the protein. The observed substitutions are generally nonconservative. All affected residues ar

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7

Lelyveld, Victor S., Wen Zhang, and Jack W. Szostak. "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proceedings of the National Academy of Sciences 117, no. 13 (2020): 7276–83. http://dx.doi.org/10.1073/pnas.1922400117.

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All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3′-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3′-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3′→P5′ phosphoramidate (NP) bonds, no such internucleot

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8

Siau, Jia Wei, Samuel Nonis, Sharon Chee, et al. "Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR)." Nucleic Acids Research 48, no. 22 (2020): e128-e128. http://dx.doi.org/10.1093/nar/gkaa933.

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Abstract Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interac

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9

Gening, L. V., S. A. Klincheva, A. Reshetnjak, A. P. Grollman, and H. Miller. "RNA aptamers selected against DNA polymerase inhibit the polymerase activities of DNA polymerases and." Nucleic Acids Research 34, no. 9 (2006): 2579–86. http://dx.doi.org/10.1093/nar/gkl326.

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10

Cann, Isaac K. O., and Yoshizumi Ishino. "Archaeal DNA Replication: Identifying the Pieces to Solve a Puzzle." Genetics 152, no. 4 (1999): 1249–67. http://dx.doi.org/10.1093/genetics/152.4.1249.

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Abstract Archaeal organisms are currently recognized as very exciting and useful experimental materials. A major challenge to molecular biologists studying the biology of Archaea is their DNA replication mechanism. Undoubtedly, a full understanding of DNA replication in Archaea requires the identification of all the proteins involved. In each of four completely sequenced genomes, only one DNA polymerase (Pol BI proposed in this review from family B enzyme) was reported. This observation suggested that either a single DNA polymerase performs the task of replicating the genome and repairing the

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11

Kanno, Tatsuo, Bruno Huettel, M. Florian Mette, et al. "Atypical RNA polymerase subunits required for RNA-directed DNA methylation." Nature Genetics 37, no. 7 (2005): 761–65. http://dx.doi.org/10.1038/ng1580.

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12

Reha-Krantz, Linda J. "Regulation of DNA Polymerase Exonucleolytic Proofreading Activity: Studies of Bacteriophage T4 “Antimutator” DNA Polymerases." Genetics 148, no. 4 (1998): 1551–57. http://dx.doi.org/10.1093/genetics/148.4.1551.

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13

Goodman, Myron F., and D. Kuchnir Fygenson. "DNA Polymerase Fidelity: From Genetics Toward a Biochemical Understanding." Genetics 148, no. 4 (1998): 1475–82. http://dx.doi.org/10.1093/genetics/148.4.1475.

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Abstract This review summarizes mutagenesis studies, emphasizing the use of bacteriophage T4 mutator and antimutator strains. Early genetic studies on T4 identified mutator and antimutator variants of DNA polymerase that, in turn, stimulated the development of model systems for the study of DNA polymerase fidelity in vitro. Later enzymatic studies using purified T4 mutator and antimutator polymerases were essential in elucidating mechanisms of base selection and exonuclease proofreading. In both cases, the base analogue 2-aminopurine (2AP) proved tremendously useful—first as a mutagen in vivo

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14

Tsurusluta, Naoya, Hisaji Maki, and Laurence Jay Korn. "Site-directed mutagenesis with Escherichia coli DNA polymerase III holoenzyme." Gene 62, no. 1 (1988): 135–39. http://dx.doi.org/10.1016/0378-1119(88)90587-2.

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15

KEOHAVONG, PHOUTHONE, ALEXANDRA G. KAT, NEAL F. CARIELLO, and WILLIAM G. THILLY. "DNA Amplification In Vitro Using T4 DNA Polymerase." DNA 7, no. 1 (1988): 63–70. http://dx.doi.org/10.1089/dna.1988.7.63.

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16

Martin, Sara K., та Richard D. Wood. "DNA polymerase ζ in DNA replication and repair". Nucleic Acids Research 47, № 16 (2019): 8348–61. http://dx.doi.org/10.1093/nar/gkz705.

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Abstract Here, we survey the diverse functions of DNA polymerase ζ (pol ζ) in eukaryotes. In mammalian cells, REV3L (3130 residues) is the largest catalytic subunit of the DNA polymerases. The orthologous subunit in yeast is Rev3p. Pol ζ also includes REV7 subunits (encoded by Rev7 in yeast and MAD2L2 in mammalian cells) and two subunits shared with the replicative DNA polymerase, pol δ. Pol ζ is used in response to circumstances that stall DNA replication forks in both yeast and mammalian cells. The best-examined situation is translesion synthesis at sites of covalent DNA lesions such as UV r

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17

Yudkina, Anna V., Evgeniy S. Shilkin, Alena V. Makarova, and Dmitry O. Zharkov. "Stalling of Eukaryotic Translesion DNA Polymerases at DNA-Protein Cross-Links." Genes 13, no. 2 (2022): 166. http://dx.doi.org/10.3390/genes13020166.

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DNA-protein cross-links (DPCs) are extremely bulky adducts that interfere with replication. In human cells, they are processed by SPRTN, a protease activated by DNA polymerases stuck at DPCs. We have recently proposed the mechanism of the interaction of DNA polymerases with DPCs, involving a clash of protein surfaces followed by the distortion of the cross-linked protein. Here, we used a model DPC, located in the single-stranded template, the template strand of double-stranded DNA, or the displaced strand, to study the eukaryotic translesion DNA polymerases ζ (POLζ), ι (POLι) and η (POLη). POL

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18

Murphy, Kelly, Hariyanto Darmawan, Amy Schultz, Elizabeth Fidalgo da Silva та Linda J. Reha-Krantz. "A method to select for mutator DNA polymerase δs in Saccharomyces cerevisiae". Genome 49, № 4 (2006): 403–10. http://dx.doi.org/10.1139/g05-106.

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Proofreading DNA polymerases share common short peptide motifs that bind Mg2+ in the exonuclease active center; however, hydrolysis rates are not the same for all of the enzymes, which indicates that there are functional and likely structural differences outside of the conserved residues. Since structural information is available for only a few proofreading DNA polymerases, we developed a genetic selection method to identify mutant alleles of the POL3 gene in Saccharomyces cerevisiae, which encode DNA polymerase δ mutants that replicate DNA with reduced fidelity. The selection procedure is bas

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19

Pospiech, Helmut, and Juhani E. Syväoja. "DNA Polymerase e - More Than a Polymerase." Scientific World JOURNAL 3 (2003): 87–104. http://dx.doi.org/10.1100/tsw.2003.08.

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This paper presents a comprehensive review of the structure and function of DNA polymerase e. Together with DNA polymerases a and d, this enzyme replicates the nuclear DNA in the eukaryotic cell. During this process, DNA polymerase a lays down RNA-DNA primers that are utilized by DNA polymerases d and e for the bulk DNA synthesis. Attempts have been made to assign these two enzymes specifically to the synthesis of the leading and the lagging strand. Alternatively, the two DNA polymerases may be needed to replicate distinct regions depending on chromatin structure. Surprisingly, the essential f

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20

Wang, Zhenghe, Irene B. Castaño, Carrie Adams, Clemence Vu, David Fitzhugh та Michael F. Christman. "Structure/Function Analysis of the Saccharomyces cerevisiae Trf4/Pol σ DNA Polymerase". Genetics 160, № 2 (2002): 381–91. http://dx.doi.org/10.1093/genetics/160.2.381.

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Abstract The Trf4p/Pol σ DNA polymerase (formerly Trf4p/Pol κ) couples DNA replication to the establishment of sister chromatid cohesion. The polymerase is encoded by two redundant homologs in Saccharomyces cerevisiae, TRF4 and TRF5, that together define a fourth essential nuclear DNA polymerase in yeast and probably in all eukaryotes. Here we present a thorough genetic analysis of the founding member of this novel family of DNA polymerases, TRF4. Analyses of mutants carrying 1 of 34 “surface-targeted” alanine scanning mutations in TRF4 have identified those regions required for Pol σ's essent

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21

López de Saro, Francisco, Roxana E. Georgescu, Frank Leu, and Mike O'Donnell. "Protein trafficking on sliding clamps." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1441 (2004): 25–30. http://dx.doi.org/10.1098/rstb.2003.1361.

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The sliding clamps of chromosomal replicases are acted upon by both the clamp loader and DNA polymerase. Several other proteins and polymerases also interact with the clamp. These proteins bind the clamp at the same spot and use it in sequential fashion. First the clamp loader must bind the clamp in order to load it onto DNA, but directly thereafter the clamp loader must clear away from the clamp so it can be used by the replicative DNA polymerase. At the end of replication, the replicase is ejected from the clamp, which presumably allows the clamp to interact with yet other proteins after its

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22

Nossal, Nancy G. "A New Look at Old Mutants of T4 DNA Polymerase." Genetics 148, no. 4 (1998): 1535–38. http://dx.doi.org/10.1093/genetics/148.4.1535.

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Abstract The DNA polymerase and nuclease activities of bacteriophage T4 DNA polymerase mutants are discussed in the context of the crystal structure of the closely related bacteriophage RB69 DNA polymerase.

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23

Reha-Krantz, L. J. "Genetic evidence for two protein domains and a potential new activity in bacteriophage T4 DNA polymerase." Genetics 124, no. 2 (1990): 213–20. http://dx.doi.org/10.1093/genetics/124.2.213.

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Abstract Intragenic complementation was detected within the bacteriophage T4 DNA polymerase gene. Complementation was observed between specific amino (N)-terminal, temperature-sensitive (ts) mutator mutants and more carboxy (C)-terminal mutants lacking DNA polymerase polymerizing functions. Protein sequences surrounding N-terminal mutation sites are similar to sequences found in Escherichia coli ribonuclease H (RNase H) and in the 5'----3' exonuclease domain of E. coli DNA polymerase I. These observations suggest that T4 DNA polymerase, like E. coli DNA polymerase I, contains a discrete N-term

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24

Wendte, Jered M., Jeremy R. Haag, Olga M. Pontes, Jasleen Singh, Sara Metcalf, and Craig S. Pikaard. "The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation." Nucleic Acids Research 47, no. 17 (2019): 9024–36. http://dx.doi.org/10.1093/nar/gkz615.

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Abstract In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV’s largest subunit given that the Pol II CTD mediates multiple aspects of Pol II transcription. We show that the CTD is dispensable for Pol IV catalytic activity and Pol IV termination-dependent activation of RNA-DEPENDENT RNA POLYMERASE 2, which partners with Pol IV to generate dsRNA precursors of the 24 nt siRNAs

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25

Yudkina, Anna V., Anton V. Endutkin, Eugenia A. Diatlova, et al. "Displacement of Slow-Turnover DNA Glycosylases by Molecular Traffic on DNA." Genes 11, no. 8 (2020): 866. http://dx.doi.org/10.3390/genes11080866.

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In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OG

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26

Shcherbakova, Polina V., та Youri I. Pavlov. "3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae". Genetics 142, № 3 (1996): 717–26. http://dx.doi.org/10.1093/genetics/142.3.717.

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Abstract The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At ea

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27

Ma, Yi, Beilei Zhang, Meng Wang, Yanghui Ou, Jufang Wang, and Shan Li. "Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site." BioMed Research International 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/2906484.

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The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) with 5′-3′ DNA polymerase activity while in absence of 5′-3′ exonuclease activity possesses high thermal stability and polymerase activity. Bst DNA polymerase was employed in isothermal multiple self-matching initiated amplification (IMSA) which amplified the interest sequence with high selectivity and was widely applied in the rapid detection of human epidemic diseases. However, the detailed information of commercial Bst DNA polymerase is unpublished and well protected by patents, which ma

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28

Ropp, Philip A., та William C. Copeland. "Cloning and Characterization of the Human Mitochondrial DNA Polymerase, DNA Polymerase γ". Genomics 36, № 3 (1996): 449–58. http://dx.doi.org/10.1006/geno.1996.0490.

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29

Iwasaki, Hiroshi, Yoshizumi Ishino, Hiroyuki Toh, Atsuo Nakata та Hideo Shinagawa. "Escherichia coli DNA polymerase II is homologous to α-like DNA polymerases". Molecular and General Genetics MGG 226-226, № 1-2 (1991): 24–33. http://dx.doi.org/10.1007/bf00273583.

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30

Hogg, Matthew, A. Elisabeth Sauer-Eriksson та Erik Johansson. "Promiscuous DNA synthesis by human DNA polymerase θ". Nucleic Acids Research 40, № 6 (2011): 2611–22. http://dx.doi.org/10.1093/nar/gkr1102.

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31

Kouji, Matsumoto, Takano Hiroyoshi, Chang I. Kim, and Hirokawa Hideo. "Primary structure of bacteriophage M2 DNA polymerase: conserved segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli." Gene 84, no. 2 (1989): 247–55. http://dx.doi.org/10.1016/0378-1119(89)90498-8.

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32

Ji, Junwei, and Anil Day. "Construction of a highly error-prone DNA polymerase for developing organelle mutation systems." Nucleic Acids Research 48, no. 21 (2020): 11868–79. http://dx.doi.org/10.1093/nar/gkaa929.

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Abstract A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation

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33

Wang, F. J., and L. S. Ripley. "DNA sequence effects on single base deletions arising during DNA polymerization in vitro by Escherichia coli Klenow fragment polymerase." Genetics 136, no. 3 (1994): 709–19. http://dx.doi.org/10.1093/genetics/136.3.709.

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Abstract Most single base deletions detected after DNA polymerization in vitro directed by either Escherichia coli DNA polymerase I or its Klenow fragment are opposite Pu in the template. The most frequent mutations were previously found to be associated with the consensus template context 5'-PyTPu-3'. In this study, the predictive power of the consensus sequence on single base deletion frequencies was directly tested by parallel comparison of mutations arising in four related DNAs differing by a single base. G, a deletion hotspot within the template context 5'-TTGA-3', was substituted by each

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34

Snyder, L., and L. Jorissen. "Escherichia coli mutations that prevent the action of the T4 unf/alc protein map in an RNA polymerase gene." Genetics 118, no. 2 (1988): 173–80. http://dx.doi.org/10.1093/genetics/118.2.173.

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Abstract Bacteriophage T4 has the substituted base hydroxymethylcytosine in its DNA and presumably shuts off host transcription by specifically blocking transcription of cytosine-containing DNA. When T4 incorporates cytosine into its own DNA, the shutoff mechanism is directed back at T4, blocking its late gene expression and phage production. Mutations which permit T4 multiplication with cytosine DNA should be in genes required for host shutoff. The only such mutations characterized thus far have been in the phage unf/alc gene. The product of this gene is also required for the unfolding of the

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35

Giot, Loïc, Roland Chanet, Michel Simon, Céline Facca та Gérard Faye. "Involvement of the Yeast DNA Polymerase δ in DNA Repair in Vivo". Genetics 146, № 4 (1997): 1239–51. http://dx.doi.org/10.1093/genetics/146.4.1239.

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The POL3 encoded catalytic subunit of DNA polymerase δ possesses a highly conserved C-terminal cysteine-rich domain in Saccharomyces cerevisiae. Mutations in some of its cysteine codons display a lethal phenotype, which demonstrates an essential function of this domain. The thermosensitive mutant pol3-13, in which a serine replaces a cysteine of this domain, exhibits a range of defects in DNA repair, such as hypersensitivity to different DNA-damaging agents and deficiency for induced mutagenesis and for recombination. These phenotypes are observed at 24°, a temperature at which DNA replication

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36

Nir Heyman, Shaked, Mika Golan, Batia Liefshitz та Martin Kupiec. "A Role for the Interactions between Polδ and PCNA Revealed by Analysis of pol3-01 Yeast Mutants". Genes 14, № 2 (2023): 391. http://dx.doi.org/10.3390/genes14020391.

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Several DNA polymerases participate in DNA synthesis during genome replication and DNA repair. PCNA, a homotrimeric ring, acts as a processivity factor for DNA polymerases. PCNA also acts as a “landing pad” for proteins that interact with chromatin and DNA at the moving fork. The interaction between PCNA and polymerase delta (Polδ) is mediated by PIPs (PCNA-interacting peptides), in particular the one on Pol32, a regulatory subunit of Polδ. Here, we demonstrate that pol3-01, an exonuclease mutant of Polδ’s catalytic subunit, exhibits a weak interaction with Pol30 compared to the WT DNA polymer

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37

Burgers, Peter M. J. "Mammalian cyclin/PCNA (DNA polymerase δ auxiliary protein) stimulates processive DNA synthesis by yeast DNA polymerase III". Nucleic Acids Research 16, № 14 (1988): 6297–307. http://dx.doi.org/10.1093/nar/16.14.6297.

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38

Beard, William A., та Samuel H. Wilson. "Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β". Mutation Research/DNA Repair 460, № 3-4 (2000): 231–44. http://dx.doi.org/10.1016/s0921-8777(00)00029-x.

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39

Yang, Han, Xiaoxin Ji, Xiao Li, et al. "Colorimetry-Based Phosphate Measurement for Polymerase Elongation." BioMed Research International 2023 (January 23, 2023): 1–13. http://dx.doi.org/10.1155/2023/8296847.

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DNA detection, which includes the measurement of variants in sequences or the presence of certain genes, is widely used in research and clinical diagnosis. Both require DNA-dependent DNA polymerase-catalyzed strand extension. Currently, these techniques rely heavily on the instruments used to visualize the results. This study introduced a simple and direct colorimetric method to measure polymerase-directed elongation. First, pyrophosphate (PPi), a by-product of strand extension, is converted into phosphate (Pi). Phosphate levels were measured using either Mo-Sb or BIOMOL Green reagent. This st

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40

Hałas, A., A. Ciesielski, and J. Zuk. "Involvement of the essential yeast DNA polymerases in induced gene conversion." Acta Biochimica Polonica 46, no. 4 (1999): 862–72. http://dx.doi.org/10.18388/abp.1999_4107.

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In the yeast Saccharomyces cerevisiae three different DNA polymerases alpha, delta and epsilon are involved in DNA replication. DNA polymerase alpha is responsible for initiation of DNA synthesis and polymerases delta and epsilon are required for elongation of DNA strand during replication. DNA polymerases delta and epsilon are also involved in DNA repair. In this work we studied the role of these three DNA polymerases in the process of recombinational synthesis. Using thermo-sensitive heteroallelic mutants in genes encoding DNA polymerases we studied their role in the process of induced gene

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41

Fidalgo da Silva, E., and L. J. Reha-Krantz. "DNA polymerase proofreading: active site switching catalyzed by the bacteriophage T4 DNA polymerase." Nucleic Acids Research 35, no. 16 (2007): 5452–63. http://dx.doi.org/10.1093/nar/gkm591.

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Arana, M. E., M. Seki, R. D. Wood, I. B. Rogozin, and T. A. Kunkel. "Low-fidelity DNA synthesis by human DNA polymerase theta." Nucleic Acids Research 36, no. 11 (2008): 3847–56. http://dx.doi.org/10.1093/nar/gkn310.

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43

Bechtereva, T. A., Y. I. Pavlov, V. I. Kramorov, B. Migunova, and O. I. Kiselev. "DNA sequencing with thermostable Tet DNA polymerase fromThermus thermophilus." Nucleic Acids Research 17, no. 24 (1989): 10507. http://dx.doi.org/10.1093/nar/17.24.10507.

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44

Rao, Venigalla B., and Nancy B. Saunders. "A rapid polymerase-chain-reaction-directed sequencing strategy using a thermostable DNA polymerase from Thermus flavus." Gene 113, no. 1 (1992): 17–23. http://dx.doi.org/10.1016/0378-1119(92)90665-c.

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45

Northam, Matthew R., Heather A. Robinson, Olga V. Kochenova та Polina V. Shcherbakova. "Participation of DNA Polymerase ζ in Replication of Undamaged DNA in Saccharomyces cerevisiae". Genetics 184, № 1 (2009): 27–42. http://dx.doi.org/10.1534/genetics.109.107482.

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46

Lelyveld, Victor S., Derek K. O’Flaherty, Lijun Zhou, Enver Cagri Izgu, and Jack W. Szostak. "DNA polymerase activity on synthetic N3′→P5′ phosphoramidate DNA templates." Nucleic Acids Research 47, no. 17 (2019): 8941–49. http://dx.doi.org/10.1093/nar/gkz707.

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Abstract Genetic polymers that could plausibly govern life in the universe might inhabit a broad swath of chemical space. A subset of these genetic systems can exchange information with RNA and DNA and could therefore form the basis for model protocells in the laboratory. N3′→P5′ phosphoramidate (NP) DNA is defined by a conservative linkage substitution and has shown promise as a protocellular genetic material, but much remains unknown about its functionality and fidelity due to limited enzymatic tools. Conveniently, we find widespread NP-DNA-dependent DNA polymerase activity among reverse tra

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47

LOGAN, KELLEY, JIMIN ZHANG, ELIZABETH A. DAVIS, and STEVEN ACKERMAN. "Drug Inhibitors of RNA Polymerase II Transcription." DNA 8, no. 8 (1989): 595–604. http://dx.doi.org/10.1089/dna.1989.8.595.

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Bezalel-Buch, Rachel, Young K. Cheun, Upasana Roy, Orlando D. Schärer та Peter M. Burgers. "Bypass of DNA interstrand crosslinks by a Rev1–DNA polymerase ζ complex". Nucleic Acids Research 48, № 15 (2020): 8461–73. http://dx.doi.org/10.1093/nar/gkaa580.

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Abstract DNA polymerase ζ (Pol ζ) and Rev1 are essential for the repair of DNA interstrand crosslink (ICL) damage. We have used yeast DNA polymerases η, ζ and Rev1 to study translesion synthesis (TLS) past a nitrogen mustard-based interstrand crosslink (ICL) with an 8-atom linker between the crosslinked bases. The Rev1–Pol ζ complex was most efficient in complete bypass synthesis, by 2–3 fold, compared to Pol ζ alone or Pol η. Rev1 protein, but not its catalytic activity, was required for efficient TLS. A dCMP residue was faithfully inserted across the ICL-G by Pol η, Pol ζ, and Rev1–Pol ζ. Re

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Wrzesiński, Michał, Anetta Nowosielska, Jadwiga Nieminuszczy, and Elzbieta Grzesiuk. "Effect of SOS-induced Pol II, Pol IV, and Pol V DNA polymerases on UV-induced mutagenesis and MFD repair in Escherichia coli cells." Acta Biochimica Polonica 52, no. 1 (2005): 139–47. http://dx.doi.org/10.18388/abp.2005_3499.

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Irradiation of organisms with UV light produces genotoxic and mutagenic lesions in DNA. Replication through these lesions (translesion DNA synthesis, TSL) in Escherichia coli requires polymerase V (Pol V) and polymerase III (Pol III) holoenzyme. However, some evidence indicates that in the absence of Pol V, and with Pol III inactivated in its proofreading activity by the mutD5 mutation, efficient TSL takes place. The aim of this work was to estimate the involvement of SOS-inducible DNA polymerases, Pol II, Pol IV and Pol V, in UV mutagenesis and in mutation frequency decline (MFD), a mechanism

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Bowman, Gregory D., Eric R. Goedken, Steven L. Kazmirski, Mike O’Donnell, and John Kuriyan. "DNA polymerase clamp loaders and DNA recognition." FEBS Letters 579, no. 4 (2004): 863–67. http://dx.doi.org/10.1016/j.febslet.2004.11.038.

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