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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. The DNA polymerases of Drosophila melanogaster. Fly (Austin) 2020; 14:49-61. [PMID: 31933406 PMCID: PMC7714529 DOI: 10.1080/19336934.2019.1710076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.
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Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Elena Speretta
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Kate Warner
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Michele Magrane
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro" , Bari, Italy
| | - Sue Cotterill
- Department Basic Medical Sciences, St Georges University London , London, UK
| | - Mitch McVey
- Department of Biology, Tufts University , Medford, MA, USA
| | - Yikang Rong
- School of Life Sciences, Sun Yat-sen University , Guangzhou, China
| | - Masamitsu Yamaguchi
- Department of Applied Biology and Advanced Insect Research Promotion Center, Kyoto Institute of Technology , Kyoto, Japan
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Leuschner C, Antranikian G. Heat-stable enzymes from extremely thermophilic and hyperthermophilic microorganisms. World J Microbiol Biotechnol 2014; 11:95-114. [PMID: 24414414 DOI: 10.1007/bf00339139] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Only in the last decade have microorganisms been discovered which grow near or above 100°C. The enzymes that are formed by these extremely thermophilic (growth temperature 65 to 85°C) and hyperthermophilic (growth temperature 85 to 110°C) microorganisms are of great interest. This review covers the extracellular and intracellular enzymes of these exotic microorganisms that have recently been described. Polymer-hydrolysing enzymes, such as amylolytic, cellulolytic, hemicellulolytic and proteolytic enzymes, will be discussed. In addition, the properties of the intracellular enzymes involved in carbohydrate and amino-acid metabolism and DNA-binding and chaperones and chaperone-like proteins from hyperthermophiles are described. Due to the unusual properties of these heat-stable enzymes, they are expected to fill the gap between biological and chemical processes.
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Su X, Zhang C, Zhao M. Discrimination of the false-positive signals of molecular beacons by combination of heat inactivation and using single walled carbon nanotubes. Biosens Bioelectron 2011; 26:3596-601. [DOI: 10.1016/j.bios.2011.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 01/22/2011] [Accepted: 02/09/2011] [Indexed: 01/03/2023]
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Kunz BA. Inhibitors of thymine nucleotide biosynthesis: antimetabolites that provoke genetic change via primary non-DNA targets. Mutat Res 1996; 355:129-40. [PMID: 8781581 DOI: 10.1016/0027-5107(96)00026-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Folate antagonists and direct-acting inhibitors of thymidylate synthase are potent genotoxic antimetabolites. These agents induce genetic change not by attacking DNA, but by interfering with the control of DNA precursor metabolism. This review surveys the genetic effects attributable to selected representatives of this class of antimetabolites.
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Affiliation(s)
- B A Kunz
- School of Biological and Chemical Sciences, Deakin University, Geelong, Victoria, Australia.
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Kunz BA, Kohalmi SE, Kunkel TA, Mathews CK, McIntosh EM, Reidy JA. International Commission for Protection Against Environmental Mutagens and Carcinogens. Deoxyribonucleoside triphosphate levels: a critical factor in the maintenance of genetic stability. Mutat Res 1994; 318:1-64. [PMID: 7519315 DOI: 10.1016/0165-1110(94)90006-x] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA precursor pool imbalances can elicit a variety of genetic effects and modulate the genotoxicity of certain DNA-damaging agents. These and other observations indicate that the control of DNA precursor concentrations is essential for the maintenance of genetic stability, and suggest that factors which offset this control may contribute to environmental mutagenesis and carcinogenesis. In this article, we review the biochemical and genetic mechanisms responsible for regulating the production and relative amounts of intracellular DNA precursors, describe the many outcomes of perturbations in DNA precursor levels, and discuss implications of such imbalances for sensitivity to DNA-damaging agents, population monitoring, and human diseases.
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Affiliation(s)
- B A Kunz
- Microbiology Department, University of Manitoba, Winnipeg, Canada
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7
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Bialek G, Grosse F. An error-correcting proofreading exonuclease-polymerase that copurifies with DNA-polymerase-alpha-primase. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53421-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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8
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Olson M, Kaguni L. 3‘–>5‘ exonuclease in Drosophila mitochondrial DNA polymerase. Substrate specificity and functional coordination of nucleotide polymerization and mispair hydrolysis. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)50067-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Lundberg KS, Shoemaker DD, Adams MW, Short JM, Sorge JA, Mathur EJ. High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene X 1991; 108:1-6. [PMID: 1761218 DOI: 10.1016/0378-1119(91)90480-y] [Citation(s) in RCA: 356] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A thermostable DNA polymerase which possesses an associated 3'-to-5' exonuclease (proofreading) activity has been isolated from the hyperthermophilic archaebacterium, Pyrococcus furiosus (Pfu). To test its fidelity, we have utilized a genetic assay that directly measures DNA polymerase fidelity in vitro during the polymerase chain reaction (PCR). Our results indicate that PCR performed with the DNA polymerase purified from P. furiosus yields amplification products containing less than 10% of the number of mutations obtained from similar amplifications performed with Taq DNA polymerase. The PCR fidelity assay is based on the amplification and cloning of lacI, lacO and lacZ alpha gene sequences (lacIOZ alpha) using either Pfu or Taq DNA polymerase. Certain mutations within the lacI gene inactivate the Lac repressor protein and permit the expression of beta Gal. When plated on a chromogenic substrate, these LacI- mutants exhibit a blue-plaque phenotype. These studies demonstrate that the error rate per nucleotide induced in the 182 known detectable sites of the lacI gene was 1.6 x 10(-6) for Pfu DNA polymerase, a greater than tenfold improvement over the 2.0 x 10(-5) error rate for Taq DNA polymerase, after approx. 10(5)-fold amplification.
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Affiliation(s)
- K S Lundberg
- Division of Research and Development, Stratagene, Inc., La Jolla, CA 92037
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Copeland W, Wang T. Catalytic subunit of human DNA polymerase alpha overproduced from baculovirus-infected insect cells. Structural and enzymological characterization. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54630-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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13
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Kohalmi SE, Glattke M, McIntosh EM, Kunz BA. Mutational specificity of DNA precursor pool imbalances in yeast arising from deoxycytidylate deaminase deficiency or treatment with thymidylate. J Mol Biol 1991; 220:933-46. [PMID: 1880805 DOI: 10.1016/0022-2836(91)90364-c] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Disruption of the dCMP deaminase (DCD1) gene, or provision of excess dTMP to a nucleotide-permeable strain, produced dramatic increases in the dCTP or dTTP pools, respectively, in growing cells of the yeast Saccharomyces cerevisiae. The mutation rate of the SUP4-o gene was enhanced 2-fold by the dCTP imbalance and 104-fold by the dTTP imbalance. 407 SUP4-o mutations that arose under these conditions, and 334 spontaneous mutations recovered in an isogenic strain having balanced DNA precursor levels, were characterized by DNA sequencing and the resulting mutational spectra were compared. Significantly more (greater than 98%) of the changes resulting from nucleotide pool imbalance were single base-pair events, the majority of which could have been due to misinsertion of the nucleotides present in excess. Unexpectedly, expanding the dCTP pool did not increase the fraction of A.T----G.C transitions relative to the spontaneous value nor did enlarging the dTTP pool enhance the proportion of G.C----A.T transitions. Instead, the elevated levels of dCTP or dTTP were associated primarily with increases in the fractions of G.C----C.G or A.T----T.A. transversions, respectively. Furthermore, T----C, and possibly A----C, events occurred preferentially in the dcd1 strain at sites where dCTP was to be inserted next. C----T and A----T events were induced most often by dTMP treatment at sites where the next correct nucleotide was dTTP or dGTP (dGTP levels were also elevated by dTMP treatment). Finally, misinsertion of dCTP or dTTP did not exhibit a strand bias. Collectively, our data suggest that increased levels of dCTP and dTTP induced mutations in yeast via nucleotide misinsertion and inhibition of proofreading but indicate that other factors must also be involved. We consider several possibilities, including potential roles for the regulation and specificity of proofreading and for mismatch correction.
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Affiliation(s)
- S E Kohalmi
- Microbiology Department, University of Manitoba, Winnipeg, Canada
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Brooke RG, Singhal R, Hinkle DC, Dumas LB. Purification and characterization of the 180- and 86-kilodalton subunits of the Saccharomyces cerevisiae DNA primase-DNA polymerase protein complex. The 180-kilodalton subunit has both DNA polymerase and 3‘—-5‘-exonuclease activities. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)49947-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Bambara RA, Jessee CB. Properties of DNA polymerases delta and epsilon, and their roles in eukaryotic DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1088:11-24. [PMID: 1846563 DOI: 10.1016/0167-4781(91)90147-e] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R A Bambara
- Department of Biochemistry, University of Rochester, NY
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Affiliation(s)
- F W Perrino
- Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle 98195
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17
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Abstract
The identities and precise roles of the DNA polymerase(s) involved in mammalian cell DNA replication are uncertain. Circumstantial evidence suggests that DNA polymerase alpha and at least one form of DNA polymerase delta, that which is stimulated by Proliferating Cell Nuclear Antigen, catalyze mammalian cell replicative DNA synthesis. Further, the in vitro properties of polymerases alpha and delta suggest a model for their coordinate action at the replication fork. The present paper summarizes the current status of DNA polymerases alpha and delta in DNA replication, and describes newly available approaches to the study of those enzymes.
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Affiliation(s)
- R V Talanian
- Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655
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19
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Meuth M. The molecular basis of mutations induced by deoxyribonucleoside triphosphate pool imbalances in mammalian cells. Exp Cell Res 1989; 181:305-16. [PMID: 2647496 DOI: 10.1016/0014-4827(89)90090-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alterations of the balanced supply of the precursors of DNA synthesis, the deoxyribonucleoside triphosphates, have dramatic genetic consequences for mammalian cells including the induction of mutations, the sensitization to DNA damaging agents, and the production of gross chromosomal abnormalities. The use of recombinant DNA techniques has allowed the analysis of some of these effects and has revealed further mechanisms by which mammalian cells control the accuracy of DNA replication.
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Affiliation(s)
- M Meuth
- Imperial Cancer Research Fund, Clare Hall Laboratories, South Mimms, Hertfordshire, United Kingdom
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21
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Perrino FW, Loeb LA. Differential extension of 3′ mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase-α. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)81697-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Characterization of a large form of DNA polymerase δ from HeLa cells that is insensitive to proliferating cell nuclear antigen. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)81640-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Busbee D, Sylvia V, Curtin G, Peng S, Srivastava V, Tilley R. Age-related changes in DNA polymerase alpha expression. Exp Gerontol 1989; 24:395-413. [PMID: 2561101 DOI: 10.1016/0531-5565(89)90047-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA polymerase alpha isozymes differing in specific activity and affinity of binding to DNA were purified from human fibroblasts derived from donors of different ages. Fetal-derived fibroblasts expressed a single, high-activity enzyme (A2), with high affinity of binding to DNA. Adult-derived fibroblasts exhibited two forms of DNA polymerase alpha, one identical to the fetal enzyme, and a second with about tenfold less activity showing low affinity of binding to DNA (A1). The ratio of DNA polymerase A2/A1 decreased dramatically with age, from 100% A2 in fetal-derived fibroblasts to about 94% A1 in fibroblasts derived from a 66-year-old donor. The DNA binding affinity of polymerase alpha A1 from adult-derived fibroblasts increased concomitant with a significant increase in activity when the enzyme was treated with phosphatidylinositol-4-monophosphate (PIP), or with inositol-1, 4-bisphosphate (I(1,4)P2). The enzyme reverted back to a less active form, with loss of the noncovalently bound I(1,4)P2, as a function of time. When permeabilized human fibroblasts with low DNA excision repair capacity were treated with 7,8-dihydrodiol-9,10-epoxybenzo(a)-pyrene (BPDE) in the presence of 32P-ATP, phosphatidylinositol, and cycloheximide, excision repair was initiated and 32P-labeled DNA polymerase alpha was recovered in the absence of de novo protein synthesis. DNA synthesis associated with either scheduled DNA synthesis or BPDE-initiated excision repair declined as a function of increased age in human cells. The data suggest that the decline in both DNA excision repair-associated and mitogen-activated DNA synthesis may be correlated with decreased total intracellular levels of DNA polymerase and with the decline in polymerase alpha activity as a function of age, that DNA repair-associated initiation of DNA synthesis in adult-derived cells may increase with activation of a pool of low activity DNA polymerase alpha, and that DNA polymerase alpha activity increases as a function of enzyme interaction with a component of the PI phosphorylation cascade.
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Affiliation(s)
- D Busbee
- Department of Anatomy, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Burgers PM. Eukaryotic DNA polymerases alpha and delta: conserved properties and interactions, from yeast to mammalian cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:235-80. [PMID: 2505329 DOI: 10.1016/s0079-6603(08)60700-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Kunkel TA, Bebenek K. Recent studies of the fidelity of DNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 951:1-15. [PMID: 2847793 DOI: 10.1016/0167-4781(88)90020-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- T A Kunkel
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
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