Journal articles: 'Gamma polymerase'

1

Milone, Margherita, and Rami Massie. "Polymerase Gamma 1 Mutations." Neurologist 16, no. 2 (March 2010): 84–91. http://dx.doi.org/10.1097/nrl.0b013e3181c78a89.

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Ji, Junwei, and Anil Day. "Construction of a highly error-prone DNA polymerase for developing organelle mutation systems." Nucleic Acids Research 48, no. 21 (November 2, 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 of 3′–5′ exonuclease function resulted in a modest 5–8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.

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3

Saneto, Russell P., and Robert K. Naviaux. "Polymerase gamma disease through the ages." Developmental Disabilities Research Reviews 16, no. 2 (August 27, 2010): 163–74. http://dx.doi.org/10.1002/ddrr.105.

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4

Konradi, Christine. "Polymerase gamma in bipolar disorder: It's complicated." Psychiatry and Clinical Neurosciences 71, no. 8 (August 2017): 507. http://dx.doi.org/10.1111/pcn.12531.

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Tzoulis, Charalampos, Gia Tuong Tran, Jonathan Coxhead, Bjørn Bertelsen, Peer K. Lilleng, Novin Balafkan, Brendan Payne, Hrvoje Miletic, Patrick F. Chinnery, and Laurence A. Bindoff. "Molecular pathogenesis of polymerase gamma–related neurodegeneration." Annals of Neurology 76, no. 1 (June 14, 2014): 66–81. http://dx.doi.org/10.1002/ana.24185.

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6

Ye, F. "The gamma subfamily of DNA polymerases: cloning of a developmentally regulated cDNA encoding Xenopus laevis mitochondrial DNA polymerase gamma." Nucleic Acids Research 24, no. 8 (April 15, 1996): 1481–88. http://dx.doi.org/10.1093/nar/24.8.1481.

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7

Kunkel, Thomas A., and Dale W. Mosbaugh. "Exonucleolytic proofreading by a mammalian DNA polymerase .gamma." Biochemistry 28, no. 3 (February 7, 1989): 988–95. http://dx.doi.org/10.1021/bi00429a011.

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8

Zhang, Ying-Hui, Ju-Sheng Lin, Yan Li, Lin-Lin Gao, and Xiao-Yan Wang. "Isolation, purification and identification of DNA polymerase gamma." World Chinese Journal of Digestology 15, no. 35 (2007): 3715. http://dx.doi.org/10.11569/wcjd.v15.i35.3715.

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9

Copeland, William C., Mikhail V. Ponamarev, Dinh Nguyen, Thomas A. Kunkel, and Matthew J. Longley. "Mutations in DNA polymerase gamma cause error prone DNA synthesis in human mitochondrial disorders." Acta Biochimica Polonica 50, no. 1 (March 31, 2003): 155–67. http://dx.doi.org/10.18388/abp.2003_3723.

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This paper summarizes recent advances in understanding the links between the cell's ability to maintain integrity of its mitochondrial genome and mitochondrial genetic diseases. Human mitochondrial DNA is replicated by the two-subunit DNA polymerase gamma (polgamma). We investigated the fidelity of DNA replication by polgamma with and without exonucleolytic proofreading and its p55 accessory subunit. Polgamma has high base substitution fidelity due to efficient base selection and exonucleolytic proofreading, but low frameshift fidelity when copying homopolymeric sequences longer than four nucleotides. Progressive external ophthalmoplegia (PEO) is a rare disease characterized by the accumulation of large deletions in mitochondrial DNA. Recently, several mutations in the polymerase and exonuclease domains of the human polgamma have been shown to be associated with PEO. We are analyzing the effect of these mutations on the human polgamma enzyme. In particular, three autosomal dominant mutations alter amino acids located within polymerase motif B of polgamma. These residues are highly conserved among family A DNA polymerases, which include T7 DNA polymerase and E.coli pol I. These PEO mutations have been generated in polgamma to analyze their effects on overall polymerase function as well as the effects on the fidelity of DNA synthesis. One mutation in particular, Y955C, was found in several families throughout Europe, including one Belgian family and five unrelated Italian families. The Y955C mutant polgamma retains a wild-type catalytic rate but suffers a 45-fold decrease in apparent binding affinity for the incoming dNTP. The Y955C derivative is also much less accurate than is wild-type polgamma, with error rates for certain mismatches elevated by 10- to 100-fold. The error prone DNA synthesis observed for the Y955C polgamma is consistent with the accumulation of mtDNA mutations in patients with PEO. The effects of other polgamma mutations associated with PEO are discussed.

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10

Harada, Ryo, Yoshihisa Hirakawa, Akinori Yabuki, Yuichiro Kashiyama, Moe Maruyama, Ryo Onuma, Petr Soukal, et al. "Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa." Pathogens 9, no. 4 (April 1, 2020): 257. http://dx.doi.org/10.3390/pathogens9040257.

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The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, “plant and protist organellar DNA polymerase (POP)” in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa—Kinetoplastea, Diplonemea, and Euglenida—to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.

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11

Lehmann Urban, Diana, Leila Motlagh Scholle, Kerstin Alt, Albert C. Ludolph, and Angela Rosenbohm. "Camptocormia as a Novel Phenotype in a Heterozygous POLG2 Mutation." Diagnostics 10, no. 2 (January 26, 2020): 68. http://dx.doi.org/10.3390/diagnostics10020068.

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Mitochondrial dysfunction is known to play a key role in the pathophysiological pathway of neurodegenerative disorders. Nuclear-encoded proteins are involved in mtDNA replication, including DNA polymerase gamma, which is the only known replicative mtDNA polymerase, encoded by nuclear genes Polymerase gamma 1 (POLG) and Polymerase gamma 2 (POLG2). POLG mutations are well-known as a frequent cause of mitochondrial myopathies of nuclear origin. However, only rare descriptions of POLG2 mutations leading to mitochondriopathies exist. Here we describe a 68-year-old woman presenting with a 20-year history of camptocormia, mild proximal weakness, and moderate CK increase. Muscle histology showed COX-negative fibres. Genetic analysis by next generation sequencing revealed an already reported heterozygous c.1192-8_1207dup24 mutation in the POLG2 gene. This is the first report on a POLG2 mutation leading to camptocormia as the main clinical phenotype, extending the phenotypic spectrum of POLG2 associated diseases. This underlines the broad phenotypic spectrum found in mitochondrial diseases, especially in mitochondrial disorders of nuclear origin.

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12

Copeland, William C., and Matthew J. Longley. "DNA Polymerase Gamma in Mitochondrial DNA Replication and Repair." Scientific World JOURNAL 3 (2003): 34–44. http://dx.doi.org/10.1100/tsw.2003.09.

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Mutations in mitochondrial DNA (mtDNA) are associated with aging, and they can cause tissue degeneration and neuromuscular pathologies known as mitochondrial diseases. Because DNA polymerase γ (pol γ) is the enzyme responsible for replication and repair of mitochondrial DNA, the burden of faithful duplication of mitochondrial DNA, both in preventing spontaneous errors and in DNA repair synthesis, falls on pol γ. Investigating the biological functions of pol γ and its inhibitors aids our understanding of the sources of mtDNA mutations. In animal cells, pol γ is composed of two subunits, a larger catalytic subunit of 125–140 kDa and second subunit of 35–55 kDa. The catalytic subunit contains DNA polymerase activity, 3’-5’ exonuclease activity, and a 5’-dRP lyase activity. The accessory subunit is required for highly processive DNA synthesis and increases the affinity of pol gamma to the DNA.

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13

Hance, Nicole, Mats I. Ekstrand, and Aleksandra Trifunovic. "Mitochondrial DNA polymerase gamma is essential for mammalian embryogenesis." Human Molecular Genetics 14, no. 13 (May 11, 2005): 1775–83. http://dx.doi.org/10.1093/hmg/ddi184.

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14

Whetsell, M., R. L. Mosley, L. Whetsell, F. V. Schaefer, K. S. Miller, and J. R. Klein. "Rearrangement and junctional-site sequence analyses of T-cell receptor gamma genes in intestinal intraepithelial lymphocytes from murine athymic chimeras." Molecular and Cellular Biology 11, no. 12 (December 1991): 5902–9. http://dx.doi.org/10.1128/mcb.11.12.5902.

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The molecular organization of rearranged T-cell receptor (TCR) gamma genes intraepithelial lymphocytes (IEL) was studied in athymic radiation chimeras and was compared with the organization of gamma gene rearrangements in IEL from thymus-bearing animals by polymerase chain reaction and by sequence analyses of DNA spanning the junction of the variable (V) and joining (J) genes. In both thymus-bearing mice and athymic chimeras, IEL V-J gamma-gene rearrangements occurred for V gamma 1.2, V gamma 2, and V gamma 5 but not for V gamma 3 or V gamma 4. Sequence analyses of cloned V-J polymerase chain reaction-amplified products indicated that in both thymus-bearing mice and athymic chimeras, rearrangement of V gamma 1.2 and V gamma 5 resulted in in-frame as well as out-of-frame genes, whereas nearly all V gamma 2 rearrangements were out of frame from either type of animal. V-segment nucleotide removal occurred in most V gamma 1.2, V gamma 2, and V gamma 5 rearrangements; J-segment nucleotide removal was common in V gamma 1.2 but not in V gamma 2 or V gamma 5 rearrangements. N-segment nucleotide insertions were present in V gamma 1.2, V gamma 2, and V gamma 5 IEL rearrangements in both thymus-bearing mice and athymic chimeras, resulting in a predominant in-frame sequence for V gamma 5 and a predominant out-of-frame sequence for V gamma 2 genes. These findings demonstrate that (i) TCR gamma-gene rearrangement occurs extrathymically in IEL, (ii) rearrangements of TCR gamma genes involve the same V gene regardless of thymus influence; and (iii) the thymus does not determine the degree to which functional or nonfunctional rearrangements occur in IEL.

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15

Whetsell, M., R. L. Mosley, L. Whetsell, F. V. Schaefer, K. S. Miller, and J. R. Klein. "Rearrangement and junctional-site sequence analyses of T-cell receptor gamma genes in intestinal intraepithelial lymphocytes from murine athymic chimeras." Molecular and Cellular Biology 11, no. 12 (December 1991): 5902–9. http://dx.doi.org/10.1128/mcb.11.12.5902-5909.1991.

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The molecular organization of rearranged T-cell receptor (TCR) gamma genes intraepithelial lymphocytes (IEL) was studied in athymic radiation chimeras and was compared with the organization of gamma gene rearrangements in IEL from thymus-bearing animals by polymerase chain reaction and by sequence analyses of DNA spanning the junction of the variable (V) and joining (J) genes. In both thymus-bearing mice and athymic chimeras, IEL V-J gamma-gene rearrangements occurred for V gamma 1.2, V gamma 2, and V gamma 5 but not for V gamma 3 or V gamma 4. Sequence analyses of cloned V-J polymerase chain reaction-amplified products indicated that in both thymus-bearing mice and athymic chimeras, rearrangement of V gamma 1.2 and V gamma 5 resulted in in-frame as well as out-of-frame genes, whereas nearly all V gamma 2 rearrangements were out of frame from either type of animal. V-segment nucleotide removal occurred in most V gamma 1.2, V gamma 2, and V gamma 5 rearrangements; J-segment nucleotide removal was common in V gamma 1.2 but not in V gamma 2 or V gamma 5 rearrangements. N-segment nucleotide insertions were present in V gamma 1.2, V gamma 2, and V gamma 5 IEL rearrangements in both thymus-bearing mice and athymic chimeras, resulting in a predominant in-frame sequence for V gamma 5 and a predominant out-of-frame sequence for V gamma 2 genes. These findings demonstrate that (i) TCR gamma-gene rearrangement occurs extrathymically in IEL, (ii) rearrangements of TCR gamma genes involve the same V gene regardless of thymus influence; and (iii) the thymus does not determine the degree to which functional or nonfunctional rearrangements occur in IEL.

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16

Seow, H. F., J. S. Rothel, L. A. Corner, and P. R. Wood. "Cloning of cervine interferon-gamma cDNA by polymerase chain reaction." New Zealand Veterinary Journal 41, no. 2 (June 1993): 91–95. http://dx.doi.org/10.1080/00480169.1993.35742.

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17

Luoma, P. T., J. Eerola, S. Ahola, A. H. Hakonen, O. Hellstrom, K. T. Kivisto, P. J. Tienari, and A. Suomalainen. "Mitochondrial DNA polymerase gamma variants in idiopathic sporadic Parkinson disease." Neurology 69, no. 11 (September 10, 2007): 1152–59. http://dx.doi.org/10.1212/01.wnl.0000276955.23735.eb.

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18

Xu, Yanming, Hongyan Huang, Xinglong Yang, and Ling Liu. "Leukoencephalopathy in mitochondrial neurogastrointestinal encephalomyopathy-like syndrome with polymerase-gamma mutations." Annals of Indian Academy of Neurology 22, no. 3 (2019): 325. http://dx.doi.org/10.4103/aian.aian_34_18.

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19

He, Quan, Christie K. Shumate, Mark A. White, Ian J. Molineux, and Y. Whitney Yin. "Exonuclease of human DNA polymerase gamma disengages its strand displacement function." Mitochondrion 13, no. 6 (November 2013): 592–601. http://dx.doi.org/10.1016/j.mito.2013.08.003.

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20

Tsuchihashi, Z., and A. Kornberg. "Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme." Proceedings of the National Academy of Sciences 87, no. 7 (April 1, 1990): 2516–20. http://dx.doi.org/10.1073/pnas.87.7.2516.

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21

Tzoulis, Charalampos, Gesche Neckelmann, Sverre J. Mørk, Bernt E. Engelsen, Carlo Viscomi, Gunnar Moen, Lars Ersland, Massimo Zeviani, and Laurence A. Bindoff. "Localized cerebral energy failure in DNA polymerase gamma-associated encephalopathy syndromes." Brain 133, no. 5 (April 16, 2010): 1428–37. http://dx.doi.org/10.1093/brain/awq067.

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22

Yang, Qin, Lydia W. M. Nausch, Georges Martin, Walter Keller, and Sylvie Doublié. "Crystal Structure of Human Poly(A) Polymerase Gamma Reveals a Conserved Catalytic Core for Canonical Poly(A) Polymerases." Journal of Molecular Biology 426, no. 1 (January 2014): 43–50. http://dx.doi.org/10.1016/j.jmb.2013.09.025.

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23

Broyles, S. S., and B. Moss. "Sedimentation of an RNA polymerase complex from vaccinia virus that specifically initiates and terminates transcription." Molecular and Cellular Biology 7, no. 1 (January 1987): 7–14. http://dx.doi.org/10.1128/mcb.7.1.7.

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A high-molecular-weight protein complex that is capable of accurate transcription initiation and termination of vaccinia virus early genes without additional factors was demonstrated. The complex was solubilized by disruption of purified virions, freed of DNA by passage through a DEAE-cellulose column, and isolated by glycerol gradient sedimentation. All detectable RNA polymerase activity was associated with the transcription complex, whereas the majority of enzymes released from virus cores including mRNA (nucleoside-2'-O)methyltransferase, poly(A) polymerase, topoisomerase, nucleoside triphosphate phosphohydrolase II, protein kinase, and single-strand DNase sedimented more slowly. Activities corresponding to two enzymes, mRNA guanylyltransferase (capping enzyme) and nucleoside triphosphate phosphohydrolase I (DNA-dependent ATPase), partially sedimented with the complex. Silver-stained polyacrylamide gels, immunoblots, and autoradiographs confirmed the presence of subunits of vaccinia virus RNA polymerase, mRNA guanylyltransferase, and nucleoside triphosphate phosphohydrolase I, as well as additional unidentified polypeptides, in fractions with transcriptase activity. A possible role for the DNA-dependent ATPase was suggested by studies with ATP analogs with gamma-S or nonhydrolyzable beta-gamma-phosphodiester bonds. These analogs were used by vaccinia virus RNA polymerase to nonspecifically transcribe single-stranded DNA templates but did not support accurate transcription of early genes by the complex. Transcription also was sensitive to high concentrations of novobiocin; however, this effect could be attributed to inhibition of RNA polymerase or ATPase activities rather than topoisomerase.

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24

Broyles, S. S., and B. Moss. "Sedimentation of an RNA polymerase complex from vaccinia virus that specifically initiates and terminates transcription." Molecular and Cellular Biology 7, no. 1 (January 1987): 7–14. http://dx.doi.org/10.1128/mcb.7.1.7-14.1987.

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A high-molecular-weight protein complex that is capable of accurate transcription initiation and termination of vaccinia virus early genes without additional factors was demonstrated. The complex was solubilized by disruption of purified virions, freed of DNA by passage through a DEAE-cellulose column, and isolated by glycerol gradient sedimentation. All detectable RNA polymerase activity was associated with the transcription complex, whereas the majority of enzymes released from virus cores including mRNA (nucleoside-2'-O)methyltransferase, poly(A) polymerase, topoisomerase, nucleoside triphosphate phosphohydrolase II, protein kinase, and single-strand DNase sedimented more slowly. Activities corresponding to two enzymes, mRNA guanylyltransferase (capping enzyme) and nucleoside triphosphate phosphohydrolase I (DNA-dependent ATPase), partially sedimented with the complex. Silver-stained polyacrylamide gels, immunoblots, and autoradiographs confirmed the presence of subunits of vaccinia virus RNA polymerase, mRNA guanylyltransferase, and nucleoside triphosphate phosphohydrolase I, as well as additional unidentified polypeptides, in fractions with transcriptase activity. A possible role for the DNA-dependent ATPase was suggested by studies with ATP analogs with gamma-S or nonhydrolyzable beta-gamma-phosphodiester bonds. These analogs were used by vaccinia virus RNA polymerase to nonspecifically transcribe single-stranded DNA templates but did not support accurate transcription of early genes by the complex. Transcription also was sensitive to high concentrations of novobiocin; however, this effect could be attributed to inhibition of RNA polymerase or ATPase activities rather than topoisomerase.

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25

Baruffini, Enrico, Fausta Serafini, Iliana Ferrero, and Tiziana Lodi. "Overexpression of DNA Polymerase Zeta Reduces the Mitochondrial Mutability Caused by Pathological Mutations in DNA Polymerase Gamma in Yeast." PLoS ONE 7, no. 3 (March 28, 2012): e34322. http://dx.doi.org/10.1371/journal.pone.0034322.

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26

Ropp, Philip A., and William C. Copeland. "Characterization of a new DNA polymerase from Schizosaccharomyces pombe: a probable homologue of the Saccharomyces cerevisiae DNA polymerase gamma." Gene 165, no. 1 (January 1995): 103–7. http://dx.doi.org/10.1016/0378-1119(95)00412-y.

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27

Lee, Seul-Ki, Ming-Hui Zhao, Zhong Zheng, Jung-Woo Kwon, Shuang Liang, Seon-Hyang Kim, Nam-Hyung Kim, and Xiang-Shun Cui. "Polymerase subunit gamma 2 affects porcine oocyte maturation and subsequent embryonic development." Theriogenology 83, no. 1 (January 2015): 121–30. http://dx.doi.org/10.1016/j.theriogenology.2014.08.019.

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28

Saleem, Ayesha, Andrew Gomez, Bart Hettinga, Justin Crane, Greg Steinberg, and Mark A. Tarnopolsky. "The effects of BDNF supplementation on polymerase gamma (POLG) 1 mutator mice." Mitochondrion 13, no. 6 (November 2013): 933–34. http://dx.doi.org/10.1016/j.mito.2013.07.091.

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29

Saleem, Ayesha, Adeel Safdar, Yu Kitaoka, Xiaoxing Ma, Olivia S. Marquez, Mahmood Akhtar, Aisha Nazli, Rahul Suri, John Turnbull, and Mark A. Tarnopolsky. "Polymerase gamma mutator mice rely on increased glycolytic flux for energy production." Mitochondrion 21 (March 2015): 19–26. http://dx.doi.org/10.1016/j.mito.2014.12.001.

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30

Tzoulis, Charalampos, Gia Tuong Tran, Thomas Schwarzlmüller, Karsten Specht, Kristoffer Haugarvoll, Novin Balafkan, Peer K. Lilleng, Hrvoje Miletic, Martin Biermann, and Laurence A. Bindoff. "Severe nigrostriatal degeneration without clinical parkinsonism in patients with polymerase gamma mutations." Brain 136, no. 8 (April 26, 2013): 2393–404. http://dx.doi.org/10.1093/brain/awt103.

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31

Farrell, Michael A., Rachel Howley, Yazan Alderazi, Francesca Brett, Joan Moroney, and Murphy Raymond. "The expanding clinical and pathologic spectrum of mitochondrial DNA polymerase gamma mutations." Journal of Neuropathology and Experimental Neurology 66, no. 5 (May 2007): 437. http://dx.doi.org/10.1097/01.jnen.0000268884.28925.df.

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32

Nolte, Kay W., Sonja Trepels-Kottek, Dagmar Honnef, Joachim Weis, Christian G. Bien, Andreas van Baalen, Klaus Ritter, et al. "Early muscle and brain ultrastructural changes in polymerase gamma 1-related encephalomyopathy." Neuropathology 33, no. 1 (April 27, 2012): 59–67. http://dx.doi.org/10.1111/j.1440-1789.2012.01317.x.

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33

Cardenas, Javier F., and R. Stephen Amato. "Compound Heterozygous Polymerase Gamma Gene Mutation in a Patient With Alpers Disease." Seminars in Pediatric Neurology 17, no. 1 (March 2010): 62–64. http://dx.doi.org/10.1016/j.spen.2010.02.012.

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34

AlJabri, Mohamed F., Naglaa M. Kamal, Abdulrahman Halabi, Haifa Korbi, Mashhour M. A. Alsayyali, and Yahea A. Alzahrani. "Lethal neonatal mitochondrial phenotype caused by a novel polymerase subunit gamma mutation." Medicine 97, no. 40 (October 2018): e12591. http://dx.doi.org/10.1097/md.0000000000012591.

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35

Wang, Z. F., Junming Yang, Z. Q. Nie, and Madeline Wu. "Purification and characterization of a .gamma.-like DNA polymerase from Chlamydomonas reinhardtii." Biochemistry 30, no. 4 (January 1991): 1127–31. http://dx.doi.org/10.1021/bi00218a034.

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36

Koczor, Christopher A., Ivan Ludlow, Earl Fields, Zhe Jiao, Tomika Ludaway, Rodney Russ, and William Lewis. "Mitochondrial polymerase gamma dysfunction and aging cause cardiac nuclear DNA methylation changes." Physiological Genomics 48, no. 4 (April 2016): 274–80. http://dx.doi.org/10.1152/physiolgenomics.00099.2015.

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Cardiomyopathy (CM) is an intrinsic weakening of myocardium with contractile dysfunction and congestive heart failure (CHF). CHF has been postulated to result from decreased mitochondrial energy production and oxidative stress. Effects of decreased mitochondrial oxygen consumption also can accelerate with aging. We previously showed DNA methylation changes in human hearts with CM. This was associated with mitochondrial DNA depletion, being another molecular marker of CM. We examined the relationship between mitochondrial dysfunction and cardiac epigenetic DNA methylation changes in both young and old mice. We used genetically engineered C57Bl/6 mice transgenic for a cardiac-specific mutant of the mitochondrial polymerase-γ (termed Y955C). Y955C mice undergo left ventricular hypertrophy (LVH) at a young age (∼94 days old), and LVH decompensated to CHF at old age (∼255 days old). Results found 95 genes differentially expressed as a result of Y955C expression, while 4,452 genes were differentially expressed as a result of aging hearts. Moreover, cardiac DNA methylation patterns differed between Y955C (4,506 peaks with 68.5% hypomethylation) and aged hearts (73,286 peaks with 80.2% hypomethylated). Correlatively, of the 95 Y955C-dependent differentially expressed genes, 30 genes (31.6%) also displayed differential DNA methylation; in the 4,452 age-dependent differentially expressed genes, 342 genes (7.7%) displayed associated DNA methylation changes. Both Y955C and aging demonstrated significant enrichment of CACGTG-associated E-box motifs in differentially methylated regions. Cardiac mitochondrial polymerase dysfunction alters nuclear DNA methylation. Furthermore, aging causes a robust change in cardiac DNA methylation that is partially associated with mitochondrial polymerase dysfunction.

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37

Nurminen, Anssi, Gregory A. Farnum, and Laurie S. Kaguni. "Pathogenicity in POLG syndromes: DNA polymerase gamma pathogenicity prediction server and database." BBA Clinical 7 (June 2017): 147–56. http://dx.doi.org/10.1016/j.bbacli.2017.04.001.

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38

Chan, Sherine S. L., and William C. Copeland. "DNA polymerase gamma and mitochondrial disease: Understanding the consequence of POLG mutations." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1787, no. 5 (May 2009): 312–19. http://dx.doi.org/10.1016/j.bbabio.2008.10.007.

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39

Poongothai, J. "Mitochondrial DNA polymerase gamma gene polymorphism is not associated with male infertility." Journal of Assisted Reproduction and Genetics 30, no. 9 (August 4, 2013): 1109–14. http://dx.doi.org/10.1007/s10815-013-0058-2.

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40

Barker, Jonathan N. W. N., Gerald D. Karabin, Tom J. Stoof, Vidya J. Sarma, Vishva M. Dixit, and Brian J. Nickoloff. "Detection of interferon-gamma mRNA in psoriatic epidermis by polymerase chain reaction." Journal of Dermatological Science 2, no. 2 (March 1991): 106–11. http://dx.doi.org/10.1016/0923-1811(91)90019-t.

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41

Silva-Pinheiro, Pedro, Carlos Pardo-Hernández, Aurelio Reyes, Lisa Tilokani, Anup Mishra, Raffaele Cerutti, Shuaifeng Li, et al. "DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion." Nucleic Acids Research 49, no. 9 (May 6, 2021): 5230–48. http://dx.doi.org/10.1093/nar/gkab282.

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Abstract Mutations in POLG, encoding POLγA, the catalytic subunit of the mitochondrial DNA polymerase, cause a spectrum of disorders characterized by mtDNA instability. However, the molecular pathogenesis of POLG-related diseases is poorly understood and efficient treatments are missing. Here, we generate the PolgA449T/A449T mouse model, which reproduces the A467T change, the most common human recessive mutation of POLG. We show that the mouse A449T mutation impairs DNA binding and mtDNA synthesis activities of POLγ, leading to a stalling phenotype. Most importantly, the A449T mutation also strongly impairs interactions with POLγB, the accessory subunit of the POLγ holoenzyme. This allows the free POLγA to become a substrate for LONP1 protease degradation, leading to dramatically reduced levels of POLγA in A449T mouse tissues. Therefore, in addition to its role as a processivity factor, POLγB acts to stabilize POLγA and to prevent LONP1-dependent degradation. Notably, we validated this mechanism for other disease-associated mutations affecting the interaction between the two POLγ subunits. We suggest that targeting POLγA turnover can be exploited as a target for the development of future therapies.

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Li, Min, Andrea C. Mislak, Yram Foli, Esinam Agbosu, Vivek Bose, Shreya Bhandari, Michal R. Szymanski, et al. "The DNA Polymerase Gamma R953C Mutant Is Associated with Antiretroviral Therapy-Induced Mitochondrial Toxicity." Antimicrobial Agents and Chemotherapy 60, no. 9 (July 5, 2016): 5608–11. http://dx.doi.org/10.1128/aac.00976-16.

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ABSTRACTWe found a heterozygous C2857T mutation (R953C) in polymerase gamma (Pol-γ) in an HIV-infected patient with mitochondrial toxicity. The R953C Pol-γ mutant binding affinity for dCTP is 8-fold less than that of the wild type. The R953C mutant shows a 4-fold decrease in discrimination of analog nucleotides relative to the wild type. R953 is located on the “O-helix” that forms the substrate deoxynucleoside triphosphate (dNTP) binding site; the interactions of R953 with E1056 and Y986 may stabilize the O-helix and affect polymerase activity.

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43

Kneba, M., I. Bolz, B. Linke, J. Bertram, D. Rothaupt, and W. Hiddemann. "Characterization of clone-specific rearrangement T-cell receptor gamma- chain genes in lymphomas and leukemias by the polymerase chain reaction and DNA sequencing." Blood 84, no. 2 (July 15, 1994): 574–81. http://dx.doi.org/10.1182/blood.v84.2.574.574.

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Abstract The structures of rearranged gamma-chain T-cell antigen receptor (TCR) genes were analyzed in 5 cases of T-cell acute lymphoblastic leukemia (T-ALL), in 15 cases of peripheral T-cell non-Hodgkin's lymphoma (T- NHL), in 1 case with large granular CD8 lymphocytosis, 1 case with CD8 lymphocytosis after autologous bone marrow transplantation for Hodgkin's disease, and in 2 cases with nonneoplastic diseases. Rearranged V-J TCR gamma-gene segments were amplified by the polymerase chain reaction (PCR). Because most of the biopsy tissue or bone marrow samples contained significant amounts of admixed nonmalignant T-cells, direct DNA sequencing of the PCR products yielded mixed sequence data because of coamplification of clonal together with polyclonal TCR gamma V-N-J junctions. Reliable data could only be obtained by cloning the V gamma-J gamma PCR products and sequencing several (4 to 10) randomly chosen clones. In the polyclonal samples, all PCR-derived clones differed in their specific V-N-J junctions, as expected. In the two T- cell lines and in most of the T-cell malignancies, monoclonal PCR products could be identified by the demonstration of clonally restricted V-N-J junctions. In most cases, this information yielded the desired clone-specific sequence and showed a background population of polyclonal TCR gamma cells in each specimen, except for those that were obtained from the T-ALL samples, the cell lines, or the NHL samples with high tumor cell fraction. The results obtained by PCR-directed sequencing were confirmed by temperature-gradient gel electrophoresis (TGGE) that showed distinct DNA bands only with the PCR products containing predominant (ie, monoclonal) TCR gamma V-N-J junctions. By combined sequence and TGGE analysis, it was found that PCR/TGGE is able to distinguish between monoclonal and polyclonal TCR gamma-PCR products. This finding prompted us to complete the analysis of the TCR gamma locus in the samples by PCR/TGGE using primer mixes which covered all possible V gamma and J gamma recombinations. Monoclonality was shown with all mixes by PCR/TGGE in 21 of 24 (87%) of the lymphoproliferations. In summary, the present study shows that the combination of amplifying TCR gamma V-N-J junctions by PCR with the identification of clonal PCR products by TGGE and DNA sequencing is a reliable method for the characterization of clonal TCR gamma sequences.

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44

Kneba, M., I. Bolz, B. Linke, J. Bertram, D. Rothaupt, and W. Hiddemann. "Characterization of clone-specific rearrangement T-cell receptor gamma- chain genes in lymphomas and leukemias by the polymerase chain reaction and DNA sequencing." Blood 84, no. 2 (July 15, 1994): 574–81. http://dx.doi.org/10.1182/blood.v84.2.574.bloodjournal842574.

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The structures of rearranged gamma-chain T-cell antigen receptor (TCR) genes were analyzed in 5 cases of T-cell acute lymphoblastic leukemia (T-ALL), in 15 cases of peripheral T-cell non-Hodgkin's lymphoma (T- NHL), in 1 case with large granular CD8 lymphocytosis, 1 case with CD8 lymphocytosis after autologous bone marrow transplantation for Hodgkin's disease, and in 2 cases with nonneoplastic diseases. Rearranged V-J TCR gamma-gene segments were amplified by the polymerase chain reaction (PCR). Because most of the biopsy tissue or bone marrow samples contained significant amounts of admixed nonmalignant T-cells, direct DNA sequencing of the PCR products yielded mixed sequence data because of coamplification of clonal together with polyclonal TCR gamma V-N-J junctions. Reliable data could only be obtained by cloning the V gamma-J gamma PCR products and sequencing several (4 to 10) randomly chosen clones. In the polyclonal samples, all PCR-derived clones differed in their specific V-N-J junctions, as expected. In the two T- cell lines and in most of the T-cell malignancies, monoclonal PCR products could be identified by the demonstration of clonally restricted V-N-J junctions. In most cases, this information yielded the desired clone-specific sequence and showed a background population of polyclonal TCR gamma cells in each specimen, except for those that were obtained from the T-ALL samples, the cell lines, or the NHL samples with high tumor cell fraction. The results obtained by PCR-directed sequencing were confirmed by temperature-gradient gel electrophoresis (TGGE) that showed distinct DNA bands only with the PCR products containing predominant (ie, monoclonal) TCR gamma V-N-J junctions. By combined sequence and TGGE analysis, it was found that PCR/TGGE is able to distinguish between monoclonal and polyclonal TCR gamma-PCR products. This finding prompted us to complete the analysis of the TCR gamma locus in the samples by PCR/TGGE using primer mixes which covered all possible V gamma and J gamma recombinations. Monoclonality was shown with all mixes by PCR/TGGE in 21 of 24 (87%) of the lymphoproliferations. In summary, the present study shows that the combination of amplifying TCR gamma V-N-J junctions by PCR with the identification of clonal PCR products by TGGE and DNA sequencing is a reliable method for the characterization of clonal TCR gamma sequences.

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45

Dallman, M. J., C. P. Larsen, and P. J. Morris. "Cytokine gene transcription in vascularised organ grafts: analysis using semiquantitative polymerase chain reaction." Journal of Experimental Medicine 174, no. 2 (August 1, 1991): 493–96. http://dx.doi.org/10.1084/jem.174.2.493.

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Cytokine gene transcription has been analyzed by direct analysis of RNA obtained from mouse heterotopic cardiac transplants. The level of expression of the cytokine genes was assessed using semiquantitative polymerase chain reaction (PCR). Expression of the cytokines investigated fell into three groups. The first group included interleukin 1 beta (IL-1 beta), IL-5, IL-6, and interferon gamma (IFN gamma). These genes were expressed in normal heart tissue at low level and were upregulated following both syngeneic and allogeneic transplantation. Genes in the second group (IL-1 alpha, IL-3) were not expressed at detectable levels in normal heart but were induced following either syngeneic or allogeneic heart grafting. IL-2, IL-4, and tumor necrosis factor beta (IFN beta) comprised the third group and these cytokines were expressed only in allogeneic grafts after transplantation.

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46

Howe, Anita Y. M., Johnathan Bloom, Carl J. Baldick, Christopher A. Benetatos, Huiming Cheng, Joel S. Christensen, Srinivas K. Chunduru, et al. "Novel Nonnucleoside Inhibitor of Hepatitis C Virus RNA-Dependent RNA Polymerase." Antimicrobial Agents and Chemotherapy 48, no. 12 (December 2004): 4813–21. http://dx.doi.org/10.1128/aac.48.12.4813-4821.2004.

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ABSTRACT A novel nonnucleoside inhibitor of hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), [(1R)-5-cyano-8-methyl-1-propyl-1,3,4,9-tetrahydropyano[3,4-b]indol-1-yl] acetic acid (HCV-371), was discovered through high-throughput screening followed by chemical optimization. HCV-371 displayed broad inhibitory activities against the NS5B RdRp enzyme, with 50% inhibitory concentrations ranging from 0.3 to 1.8 μM for 90% of the isolates derived from HCV genotypes 1a, 1b, and 3a. HCV-371 showed no inhibitory activity against a panel of human polymerases, including mitochondrial DNA polymerase gamma, and other unrelated viral polymerases, demonstrating its specificity for the HCV polymerase. A single administration of HCV-371 to cells containing the HCV subgenomic replicon for 3 days resulted in a dose-dependent reduction of the steady-state levels of viral RNA and protein. Multiple treatments with HCV-371 for 16 days led to a >3-log10 reduction in the HCV RNA level. In comparison, multiple treatments with a similar inhibitory dose of alpha interferon resulted in a 2-log10 reduction of the viral RNA level. In addition, treatment of cells with a combination of HCV-371 and pegylated alpha interferon resulted in an additive antiviral activity. Within the effective antiviral concentrations of HCV-371, there was no effect on cell viability and metabolism. The intracellular antiviral specificity of HCV-371 was demonstrated by its lack of activity in cells infected with several DNA or RNA viruses. Fluorescence binding studies show that HCV-371 binds the NS5B with an apparent dissociation constant of 150 nM, leading to high selectivity and lack of cytotoxicity in the antiviral assays.

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47

Bantia, S., SM Mane, WR Bell, and CV Dang. "Fibrinogen Baltimore I: polymerization defect associated with a gamma 292Gly----Val (GGC----GTC) mutation." Blood 76, no. 11 (December 1, 1990): 2279–83. http://dx.doi.org/10.1182/blood.v76.11.2279.2279.

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Abstract Fibrinogen Baltimore I is one of the very first congenital abnormal fibrinogens reported over several decades ago; however, the molecular defect of this dysfibrinogen has eluded identification. In fact, several reports misidentified the functional defect of Baltimore I, which has impaired fibrin monomer polymerization. Reversed-phase high- performance liquid chromatography analysis of lysyl endopeptidase digest of the purified Baltimore I gamma-chain showed an abnormal peptide not found in the co-existing normal gamma-chain of this heterozygote. Amino acid sequencing of this peptide indicated that gamma-chain Gly292 is replaced by valine. This observation was confirmed, and the genetic defect was determined by direct nucleotide sequencing of a polymerase chain reaction product containing codon gamma 292, which is mutated: GGC----GTC. The molecular defect of Fibrinogen Baltimore I lies in a region of the gamma-chain required for fibrin polymerization, suggesting that the integrity of gamma Gly292 is critical for fibrin assembly.

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48

Bantia, S., SM Mane, WR Bell, and CV Dang. "Fibrinogen Baltimore I: polymerization defect associated with a gamma 292Gly----Val (GGC----GTC) mutation." Blood 76, no. 11 (December 1, 1990): 2279–83. http://dx.doi.org/10.1182/blood.v76.11.2279.bloodjournal76112279.

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Fibrinogen Baltimore I is one of the very first congenital abnormal fibrinogens reported over several decades ago; however, the molecular defect of this dysfibrinogen has eluded identification. In fact, several reports misidentified the functional defect of Baltimore I, which has impaired fibrin monomer polymerization. Reversed-phase high- performance liquid chromatography analysis of lysyl endopeptidase digest of the purified Baltimore I gamma-chain showed an abnormal peptide not found in the co-existing normal gamma-chain of this heterozygote. Amino acid sequencing of this peptide indicated that gamma-chain Gly292 is replaced by valine. This observation was confirmed, and the genetic defect was determined by direct nucleotide sequencing of a polymerase chain reaction product containing codon gamma 292, which is mutated: GGC----GTC. The molecular defect of Fibrinogen Baltimore I lies in a region of the gamma-chain required for fibrin polymerization, suggesting that the integrity of gamma Gly292 is critical for fibrin assembly.

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49

Ikuta, K., and I. L. Weissman. "The junctional modifications of a T cell receptor gamma chain are determined at the level of thymic precursors." Journal of Experimental Medicine 174, no. 5 (November 1, 1991): 1279–82. http://dx.doi.org/10.1084/jem.174.5.1279.

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T precursors from fetal liver and adult bone marrow were compared for their ability to give rise to V gamma 4+ T cell development. Fetal thymic lobes were repopulated with fetal liver or adult bone marrow cells, and the organ-cultured thymocytes were analyzed for their T cell receptor expression by the polymerase chain reaction (PCR). Both day 14 fetal liver and adult bone marrow cells gave rise to thymocytes with V gamma 4-J gamma 1 transcripts. However, the average size of the PCR products derived from adult precursors was slightly larger than that from fetal precursors. DNA sequence analysis of the V gamma 4-J gamma 1 transcripts showed that early fetal liver precursors predominantly gave rise to thymocytes with the V gamma 4-J gamma 1 transcripts without N nucleotide insertion, while late fetal liver and adult marrow precursors predominantly gave rise to thymocytes with modified V gamma 4-J gamma 1 junctions. These results suggest the possibility that the level of the N nucleotide insertion is programmed at the level of thymic precursors. This study also supported the model presented previously that the developmental potential of hematopoietic stem cells may change during ontogeny.

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50

Bentley, Steven R., Jianguo Shan, Michael Todorovic, Stephen A. Wood, and George D. Mellick. "Rare POLG1 CAG variants do not influence Parkinson's disease or polymerase gamma function." Mitochondrion 15 (March 2014): 65–68. http://dx.doi.org/10.1016/j.mito.2014.01.004.

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Journal articles on the topic 'Gamma polymerase'

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