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Journal articles on the topic 'Polymerasa'

Author: Grafiati

Published: 28 June 2021

Last updated: 29 July 2025

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1

Milanova, E., J. Naumov, M. Stojovski, G. Petrovska, E. Nikolovska, and S. Stojkovska. "HPV TYPES DETECTED WITH POLYMERASA-CHAIN REACTION IN DETECTION OF PRECANCEROUS LESIONS ON THE CERVIX OF THE UTERUS." International Journal of Gynecologic Cancer 14, Suppl 1 (2004): 179.3–179. http://dx.doi.org/10.1136/ijgc-00009577-200409001-00644.

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2

Panjkovic, Milana, and Tatjana Ivkovic-Kapicl. "Etiology and pathogenesis of precancerous lesions and invasive cervical carcinoma." Medical review 61, no. 7-8 (2008): 364–68. http://dx.doi.org/10.2298/mpns0808364p.

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Cervical cancer is the second most common gynecological malignancy in the world. Human papilloma virus (HPV) infection is the leading ethiologic agent in the development of premalignant and malignant cervical diseases. HPV is a member of the Papovaviridae family and until now over 100 types have been recognized. There are two types of viral infection: latent and productive. Virus induced oncogenesis is the result of interaction between virus oncoproteins E6 and E7 and tumor supresor host genes p53 and Rb. Many cofactors such as immunosuppression, early sexual relationship, multiple sexual part

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3

Vidić, Branka, Stanko Boboš, Sara Savić, and Živoslav Grgić. "MYCOPLASMA AS THE CAUSE OF INFECTIONS IN CATTLE." Archives of Veterinary Medicine 5, no. 2 (2012): 11–18. http://dx.doi.org/10.46784/e-avm.v5i2.166.

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During the last few years more than 20 different types of Mycoplasma, Ureaplasma and Acholeplasma microorganisms have been isolated from cattle with different clinical signs. Most of Mycoplasma microorganisms have a secondary role in the appearance of infection in cattle. Differently, Mycoplasma bovis (M. bovis) has a primary role in the infection of cattle. It has been proved that M. bovis frequently causes pneumonia, mastitis and arthritis in cows. Besides, M. bovis is identified as a causative agent in meningitis, middle ear infection, keratoconjunctivitis, decubitus abscesses, vaginitis an

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4

Guidetto, Betiana Alejandra, Sebastian Fonseca, Alejandro Martin Abrate, and Maria Teresa Politi. "Valor predictivo de proteína C reactiva al ingreso sanatorial y requerimiento de asistencia respiratoria mecánica en adultos internados por COVID-19." Revista de la Facultad de Ciencias Médicas de Córdoba 81, no. 1 (2024): 67–82. http://dx.doi.org/10.31053/1853.0605.v81.n1.41799.

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Introducción: Durante la pandemia por COVID-19, los pacientes con peor evolución presentaron deterioro clínico a los 7-10 días del inicio de síntomas, lo cual sugiere que la respuesta inflamatoria podría participar de la fisiopatogenia de la enfermedad. El objetivo de este estudio fue evaluar la asociación entre los valores de proteína C reactiva (PCr) en plasma al ingreso sanatorial en adultos con COVID-19 y el requerimiento de asistencia respiratoria mecánica (ARM) durante la internación. Métodos: Cohorte retrospectiva, observacional, en un centro privado de la provincia de Buenos Aire

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5

Peramachi Palanivelu. "Identification of Polymerase and Proofreading Exonuclease Domains in the DNA Polymerases IA, IB and Nuclear-Encoded RNA Polymerase of the Plant Chloroplasts." World Journal of Advanced Research and Reviews 17, no. 3 (2023): 706–27. http://dx.doi.org/10.30574/wjarr.2023.17.3.0455.

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Chloroplast plays a crucial role in all photosynthetic plants and converts the light energy to chemical energy. It is a semi-autonomous organelle and is mostly controlled by its own genome and partly by the nuclear imports. To replicate its own genome, it uses two DNA polymerases, viz. polymerases IA and IB. DNA polymerase IA showed 72.45% identity to polymerase IB, but only 35.35% identity to the E. coli DNA polymerase I. Multiple sequence alignment (MSA) analysis have shown that the DNA polymerases IA and IB and the E. coli DNA polymerase I possess almost identical active sites for polymeriz

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6

Gibbs, J. S., K. Weisshart, P. Digard, A. deBruynKops, D. M. Knipe, and D. M. Coen. "Polymerization activity of an alpha-like DNA polymerase requires a conserved 3'-5' exonuclease active site." Molecular and Cellular Biology 11, no. 9 (1991): 4786–95. http://dx.doi.org/10.1128/mcb.11.9.4786-4795.1991.

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Most DNA polymerases are multifunctional proteins that possess both polymerizing and exonucleolytic activities. For Escherichia coli DNA polymerase I and its relatives, polymerase and exonuclease activities reside on distinct, separable domains of the same polypeptide. The catalytic subunits of the alpha-like DNA polymerase family share regions of sequence homology with the 3'-5' exonuclease active site of DNA polymerase I; in certain alpha-like DNA polymerases, these regions of homology have been shown to be important for exonuclease activity. This finding has led to the hypothesis that alpha

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7

Gibbs, J. S., K. Weisshart, P. Digard, A. deBruynKops, D. M. Knipe, and D. M. Coen. "Polymerization activity of an alpha-like DNA polymerase requires a conserved 3'-5' exonuclease active site." Molecular and Cellular Biology 11, no. 9 (1991): 4786–95. http://dx.doi.org/10.1128/mcb.11.9.4786.

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Most DNA polymerases are multifunctional proteins that possess both polymerizing and exonucleolytic activities. For Escherichia coli DNA polymerase I and its relatives, polymerase and exonuclease activities reside on distinct, separable domains of the same polypeptide. The catalytic subunits of the alpha-like DNA polymerase family share regions of sequence homology with the 3'-5' exonuclease active site of DNA polymerase I; in certain alpha-like DNA polymerases, these regions of homology have been shown to be important for exonuclease activity. This finding has led to the hypothesis that alpha

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8

Peramachi, Palanivelu. "Identification of Polymerase and Proofreading Exonuclease Domains in the DNA Polymerases IA, IB and Nuclear-Encoded RNA Polymerase of the Plant Chloroplasts." World Journal of Advanced Research and Reviews 17, no. 3 (2023): 706–27. https://doi.org/10.5281/zenodo.8134229.

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Chloroplast plays a crucial role in all photosynthetic plants and converts the light energy to chemical energy. It is a semi-autonomous organelle and is mostly controlled by its own genome and partly by the nuclear imports. To replicate its own genome, it uses two DNA polymerases, viz. polymerases IA and IB. DNA polymerase IA showed 72.45% identity to polymerase IB, but only 35.35% identity to the <em>E. coli</em> DNA polymerase I. Multiple sequence alignment (MSA) analysis have shown that the DNA polymerases IA and IB and the <em>E. coli</em> DNA polymerase I possess almos

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9

Jadranin, Zeljko, Vesna Suljagic, Veljko Todorovic, Miroljub Trkuljic, and Dusan Vucetic. "HIV/AIDS and other sexually transmitted infections among military members of the armed forces of Serbia." Vojnosanitetski pregled 69, no. 1 (2012): 43–48. http://dx.doi.org/10.2298/vsp1201043j.

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Background/Aim. Military personnel is a population group at special risk of exposure to sexually transmitted diseases (STD). In peacetime, STD infection rates among service members are generally 2 to 5 times higher than among civilian population. In time of conflict, the differences can be 50 or more times greater. This study describes sexual behavior as a risk factor for STD in the Armed Forces of Serbia. Methods. The sample of 5 617 voluntary blood donors from the Armed Forces of Serbia gave blood and filled World Health Organization Questionnaire about sexual behavior within January 2007 -

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10

Raia, Pierre, Marc Delarue, and Ludovic Sauguet. "An updated structural classification of replicative DNA polymerases." Biochemical Society Transactions 47, no. 1 (2019): 239–49. http://dx.doi.org/10.1042/bst20180579.

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AbstractReplicative DNA polymerases are nano-machines essential to life, which have evolved the ability to copy the genome with high fidelity and high processivity. In contrast with cellular transcriptases and ribosome machines, which evolved by accretion of complexity from a conserved catalytic core, no replicative DNA polymerase is universally conserved. Strikingly, four different families of DNA polymerases have evolved to perform DNA replication in the three domains of life. In Bacteria, the genome is replicated by DNA polymerases belonging to the A- and C-families. In Eukarya, genomic DNA

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11

Walsh, Jason M., and Penny J. Beuning. "Synthetic Nucleotides as Probes of DNA Polymerase Specificity." Journal of Nucleic Acids 2012 (2012): 1–17. http://dx.doi.org/10.1155/2012/530963.

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The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example,Escherichia coliDNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more r

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12

Miura, Masashi, Chihiro Tanigawa, Yoshito Fujii, and Satoshi Kaneko. "COMPARISON OF SIX COMMERCIALLY-AVAILABLE DNA POLYMERASES FOR DIRECT PCR." Revista do Instituto de Medicina Tropical de São Paulo 55, no. 6 (2013): 401–6. http://dx.doi.org/10.1590/s0036-46652013000600005.

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SUMMARY The use of a “direct PCR” DNA polymerase enables PCR amplification without any prior DNA purification from blood samples due to the enzyme's resistance to inhibitors present in blood components. Such DNA polymerases are now commercially available. We compared the PCR performance of six direct PCR-type DNA polymerases (KOD FX, Mighty Amp, Hemo KlenTaq, Phusion Blood II, KAPA Blood, and BIOTAQ) in dried blood eluted from a filter paper with TE buffer. GoTaq Flexi was used as a standard DNA polymerase. PCR performance was evaluated by a nested PCR technique for detecting Plasmodium falcip

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13

Jung, G. H., M. C. Leavitt, J. C. Hsieh, and J. Ito. "Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases." Proceedings of the National Academy of Sciences 84, no. 23 (1987): 8287–91. http://dx.doi.org/10.1073/pnas.84.23.8287.

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14

Choi, Jeong Jin, Jae-Geun Song, Ki Hoon Nam, et al. "Unique Substrate Spectrum and PCR Application of Nanoarchaeum equitans Family B DNA Polymerase." Applied and Environmental Microbiology 74, no. 21 (2008): 6563–69. http://dx.doi.org/10.1128/aem.00624-08.

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ABSTRACT The known archaeal family B DNA polymerases are unable to participate in the PCR in the presence of uracil. Here, we report on a novel archaeal family B DNA polymerase from Nanoarchaeum equitans that can successfully utilize deaminated bases such as uracil and hypoxanthine and on its application to PCR. N. equitans family B DNA polymerase (Neq DNA polymerase) produced λ DNA fragments up to 10 kb with an approximately 2.2-fold-lower error rate (5.53 ï¿½ 10−6) than Taq DNA polymerase (11.98 ï¿½ 10−6). Uniquely, Neq DNA polymerase also amplified λ DNA fragments using dUTP (in place of dT

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15

Davalieva, Katarina, and Georgi D. Efremov. "Influence of salts and pcr inhibitors on the amplification capacity of three thermostable DNA polymerases." Macedonian Journal of Chemistry and Chemical Engineering 29, no. 1 (2010): 57. http://dx.doi.org/10.20450/mjcce.2010.173.

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The full potential of PCR as a rapid DNA detection method, is limited by inhibition of thermostable DNA polymerases by components in biological samples and substances used for purification of template DNA. We compared the inhibition effect of blood, phenol and various ions on Taq, Tth and Tne thermostable DNA polymerases prepared by us. The amplification capacity of DNA polymerases was tested on the amplification of a 631 bp fragment of a â- globin gene from a 100 ng DNA template under the optimal PCR buffer. Blood above 1 % (v/v) and phenol above 0.1 % (v/v) inhibited Taq, while Tne and Tth t

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16

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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17

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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18

Gaillard, Richard K., Jennifer Barnard, Vincent Lopez, et al. "Kinetic Analysis of Wild-Type and YMDD Mutant Hepatitis B Virus Polymerases and Effects of Deoxyribonucleotide Concentrations on Polymerase Activity." Antimicrobial Agents and Chemotherapy 46, no. 4 (2002): 1005–13. http://dx.doi.org/10.1128/aac.46.4.1005-1013.2002.

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ABSTRACT Mutations in the YMDD motif of the hepatitis B virus (HBV) DNA polymerase result in reduced susceptibility of HBV to inhibition by lamivudine, at a cost in replication fitness. The mechanisms underlying the effects of YMDD mutations on replication fitness were investigated using both a cell-based viral replication system and an in vitro enzyme assay to examine wild-type (wt) and YMDD-mutant polymerases. We calculated the affinities of wt and YMDD-mutant polymerases for each natural deoxyribonucleoside triphosphate (dNTP) and determined the intracellular concentrations of each dNTP in

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19

Budd, M. E., and J. L. Campbell. "DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae." Molecular and Cellular Biology 15, no. 4 (1995): 2173–79. http://dx.doi.org/10.1128/mcb.15.4.2173.

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The ability of yeast DNA polymerase mutant strains to carry out repair synthesis after UV irradiation was studied by analysis of postirradiation molecular weight changes in cellular DNA. Neither DNA polymerase alpha, delta, epsilon, nor Rev3 single mutants evidenced a defect in repair. A mutant defective in all four of these DNA polymerases, however, showed accumulation of single-strand breaks, indicating defective repair. Pairwise combination of polymerase mutations revealed a repair defect only in DNA polymerase delta and epsilon double mutants. The extent of repair in the double mutant was

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20

Harada, Ryo, Yoshihisa Hirakawa, Akinori Yabuki, et al. "Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa." Pathogens 9, no. 4 (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 mitoch

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Cohen, Susan E., Veronica G. Godoy, and Graham C. Walker. "Transcriptional Modulator NusA Interacts with Translesion DNA Polymerases in Escherichia coli." Journal of Bacteriology 191, no. 2 (2008): 665–72. http://dx.doi.org/10.1128/jb.00941-08.

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ABSTRACT NusA, a modulator of RNA polymerase, interacts with the DNA polymerase DinB. An increased level of expression of dinB or umuDC suppresses the temperature sensitivity of the nusA11 strain, requiring the catalytic activities of these proteins. We propose that NusA recruits translesion DNA synthesis (TLS) polymerases to RNA polymerases stalled at gaps, coupling TLS to transcription.

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22

Thomsen, Darrell R., Nancee L. Oien, Todd A. Hopkins, et al. "Amino Acid Changes within Conserved Region III of the Herpes Simplex Virus and Human Cytomegalovirus DNA Polymerases Confer Resistance to 4-Oxo-Dihydroquinolines, a Novel Class of Herpesvirus Antiviral Agents." Journal of Virology 77, no. 3 (2003): 1868–76. http://dx.doi.org/10.1128/jvi.77.3.1868-1876.2003.

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ABSTRACT The 4-oxo-dihydroquinolines (PNU-182171 and PNU-183792) are nonnucleoside inhibitors of herpesvirus polymerases (R. J. Brideau et al., Antiviral Res. 54:19-28, 2002; N. L. Oien et al., Antimicrob. Agents Chemother. 46:724-730, 2002). In cell culture these compounds inhibit herpes simplex virus type 1 (HSV-1), HSV-2, human cytomegalovirus (HCMV), varicella-zoster virus (VZV), and human herpesvirus 8 (HHV-8) replication. HSV-1 and HSV-2 mutants resistant to these drugs were isolated and the resistance mutation was mapped to the DNA polymerase gene. Drug resistance correlated with a poin

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Coello-Coutiño, P., E. García-Ramírez, and J. M. Vázquez-Ramos. "Preparation of an antibody against a maize DNA polymerase holoenzyme: identification of the polymerase catalytic subunit." Canadian Journal of Botany 72, no. 6 (1994): 818–22. http://dx.doi.org/10.1139/b94-104.

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Three different DNA polymerase activities can be separated from germinating maize axes through DEAE – cellulose chromatography. Of these, DNA polymerase 2 appears to be a replicative-type enzyme composed of several subunits. An antibody has been developed against the DNA polymerase 2 multisubunit complex, which mainly recognizes a polypeptide of molecular weight around 90 kDa. Polypeptides of molecular mass of 83, 70, 60, 55, 45, and 24 kDa are also recognized. Activity gels showed that the 90-kDa polypeptide possesses catalytic activity. DNA polymerases 1 and 3 are not recognized by the antib

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Maul, Robert W., and Mark D. Sutton. "Roles of the Escherichia coli RecA Protein and the Global SOS Response in Effecting DNA Polymerase Selection In Vivo." Journal of Bacteriology 187, no. 22 (2005): 7607–18. http://dx.doi.org/10.1128/jb.187.22.7607-7618.2005.

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ABSTRACT The Escherichia coli β sliding clamp protein is proposed to play an important role in effecting switches between different DNA polymerases during replication, repair, and translesion DNA synthesis. We recently described how strains bearing the dnaN159 allele, which encodes a mutant form of the β clamp (β159), display a UV-sensitive phenotype that is suppressed by inactivation of DNA polymerase IV (M. D. Sutton, J. Bacteriol. 186:6738-6748, 2004). As part of an ongoing effort to understand mechanisms of DNA polymerase management in E. coli, we have further characterized effects of the

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Bettiol, Michael F., Randall T. Irvin, and Paul A. Horgen. "Immunological analyses of selected eukaryotic RNA polymerases II." Canadian Journal of Biochemistry and Cell Biology 63, no. 12 (1985): 1217–30. http://dx.doi.org/10.1139/o85-153.

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Polyclonal antibodies to native RNA polymerase II of Achlya ambisexualis and Agaricus bisporus were produced in rabbits and in mice. Monoclonal antibodies were produced against the α-amanitin resistant RNA polymerase II of the mushroom A. bisporus. These antibodies were used in comparative cross-reactivity studies with five purified RNA polymerases II (A. bisporus, A. ambisexualis, Saccharomyces cerevisiae, wheat germ, and calf thymus). A method for quantitatively comparing cross-reactivity was developed utilizing an enzyme-linked immunosorbant assay (ELISA). ELIS A comparisons indicated that

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Yamaguchi, Masamitsu, and Sue Cotterill. "Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies." International Journal of Molecular Sciences 24, no. 9 (2023): 8078. http://dx.doi.org/10.3390/ijms24098078.

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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 mec

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LEHMANN, A., A. NIIMI, T. OGI, et al. "Translesion synthesis: Y-family polymerases and the polymerase switch." DNA Repair 6, no. 7 (2007): 891–99. http://dx.doi.org/10.1016/j.dnarep.2007.02.003.

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McIntyre, Justyna. "Polymerase iota - an odd sibling among Y family polymerases." DNA Repair 86 (February 2020): 102753. http://dx.doi.org/10.1016/j.dnarep.2019.102753.

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Jensen, Grant J., Gavin Meredith, David A. Bushnell, and Roger D. Kornberg. "Structure of Wild Type Yeast RNA Polymerase II and Location of RPB4 and RPB7." Microscopy and Microanalysis 4, S2 (1998): 972–73. http://dx.doi.org/10.1017/s1431927600024983.

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Nucleic acid polymerase structure has been studied by both X-ray and electron crystallography. To date, only the smaller, single subunit polymerases have been subjected to X-ray analysis, including the bacteriophage T7 RNA polymerase, which is the only RNA polymerase whose structure is known to atomic resolution. Lower resolution structures of several multisubunit polymerases have been determined by electron crystallography, including a mutant form of yeast RNA polymerase II which lacks subunits Rpb4 and Rpb7 (denoted A4/7 polymerase). All polymerase structures obtained by both X-ray and elect

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Crotty, Shane, David Gohara, Devin K. Gilligan, Sveta Karelsky, Craig E. Cameron, and Raul Andino. "Manganese-Dependent Polioviruses Caused by Mutations within the Viral Polymerase." Journal of Virology 77, no. 9 (2003): 5378–88. http://dx.doi.org/10.1128/jvi.77.9.5378-5388.2003.

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ABSTRACT Viral RNA-dependent RNA polymerases exhibit great sequence diversity. Only six core amino acids are conserved across all polymerases of positive-strand RNA viruses of eukaryotes. While exploring the function of one of these completely conserved residues, asparagine 297 in the prototypic poliovirus polymerase 3Dpol, we identified three viable mutants with noncanonical amino acids at this conserved position. Although asparagine 297 could be replaced by glycine or alanine in these mutants, the viruses exhibited Mn2+-dependent RNA replication and viral growth. All known RNA polymerases an

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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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Bridges, B. A., Helen Bates, and Firdaus Sharif. "Polymerases and UV mutagenesis in Escherichia coli." Genome 31, no. 2 (1989): 572–77. http://dx.doi.org/10.1139/g89-106.

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Evidence for and against the involvement of the known nucleic acid polymerases in UV mutagenesis in Escherichia coli is reviewed. There is no evidence that rules out the participation of any of them when they are present but only one, the α subunit of DNA polymerase III holoenzyme (polC gene product) has been shown to be essential. It is argued that the PolC protein that functions in UV mutagenesis may not be immediately recognizable as one of the normal cellular polymerases or polymerase complexes.Key words: polymerases, ultraviolet light, mutagenesis, DNA repair, misincorporation.

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Egorova, Tatiana, Ekaterina Shuvalova, Sabina Mukba, Alexey Shuvalov, Peter Kolosov, and Elena Alkalaeva. "Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides." International Journal of Molecular Sciences 22, no. 10 (2021): 5186. http://dx.doi.org/10.3390/ijms22105186.

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Pairs of unnatural nucleotides are used to expand the genetic code and create artificial DNA or RNA templates. In general, an approach is used to engineer orthogonal systems capable of reading codons comprising artificial nucleotides; however, DNA and RNA polymerases capable of recognizing unnatural nucleotides are required for amplification and transcription of templates. Under favorable conditions, in the presence of modified nucleotide triphosphates, DNA polymerases are able to synthesize unnatural DNA with high efficiency; however, the currently available RNA polymerases reveal high specif

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McInerney, Peter, Paul Adams, and Masood Z. Hadi. "Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase." Molecular Biology International 2014 (August 17, 2014): 1–8. http://dx.doi.org/10.1155/2014/287430.

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As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR a

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Pavlov, Youri I., Anna S. Zhuk, and Elena I. Stepchenkova. "DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer." Cancers 12, no. 12 (2020): 3489. http://dx.doi.org/10.3390/cancers12123489.

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Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named “division of labor,” remains standing, with an amendment of the broader role of polymerase δ in the replication of both t

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Core, Leighton J., Joshua J. Waterfall, and John T. Lis. "Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters." Science 322, no. 5909 (2008): 1845–48. http://dx.doi.org/10.1126/science.1162228.

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RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an or

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Nguyen, Khanh Tan, Hung Manh Tran, Anh Tuan Trieu, Van Thi Huynh Nguyen, Hoang M. Nguyen, and Phu Tran Vinh Phu. "PURIFICATION AND ANALYSIS CATALYTIC FUNCTIONS OF RECOMBINANT INFLUENZA VIRAL POLYMERASES." Journal of microbiology, biotechnology and food sciences 11, no. 4 (2022): e4954. http://dx.doi.org/10.55251/jmbfs.4954.

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Polymerase of influenza virus is made up of three subunits PB1, PB2, and PA, which are involved in viral genome transcription and replication. Purification of sufficient amounts of viral polymerase is essential to understand the catalytic function of viral polymerase. In this study, we generated a viral polymerase expression system in human embryonic kidney 293T cells (293T cells). The cDNAs for RNA segments 1, 2, and 3, which encode for PB2, PB1, and PA proteins, respectively, were integrated into the mammalian expression plasmids pCAGGS to simultaneously express all viral polymerase proteins

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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 (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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McDonald, John P., Agnès Tissier, Ekaterina G. Frank, Shigenori Iwai, Fumio Hanaoka, and Roger Woodgate. "DNA polymerase iota and related Rad30–like enzymes." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356, no. 1405 (2001): 53–60. http://dx.doi.org/10.1098/rstb.2000.0748.

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Until recently, the molecular mechanisms of translesion DNA synthesis (TLS), a process whereby a damaged base is used as a template for continued replication, was poorly understood. This area of scientific research has, however, been revolutionized by the finding that proteins long implicated in TLS are, in fact, DNA polymerases. Members of this so–called UmuC/DinB/Rev1/Rad30 superfamily of polymerases have been identified in prokaryotes, eukaryotes and archaea. Biochemical studies with the highly purified polymerases reveal that some, but not all, can traverse blocking lesions in template DNA

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Pan, Junhua, Vikram N. Vakharia, and Yizhi Jane Tao. "The structure of a birnavirus polymerase reveals a distinct active site topology." Proceedings of the National Academy of Sciences 104, no. 18 (2007): 7385–90. http://dx.doi.org/10.1073/pnas.0611599104.

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Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the RNA recognition motif (RRM) found in many RNA-binding proteins. Considering that polymerases have well conserved structures, it was surprising that the RNA-dependent RNA polymerases from birnaviruses, a group of dsRNA viruses, have their catalytic motifs arranged in a permuted order in sequence. Here we report the 2.5 Å structure of a birnavirus VP

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Antipov, A. D., and N. E. Zlobin. "The Efficiency of Various DNA Polymerases for Amplification of Long Sequences from Genomic DNA and cDNA of Cultivated Potato." Прикладная биохимия и микробиология 59, no. 4 (2023): 392–400. http://dx.doi.org/10.31857/s0555109923040025.

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Amplification of long fragments from complex templates, such as eukaryotic genomic DNA, is considered a difficult task for most DNA polymerases. In this research, 6 variants of DNA polymerases were used to amplify full-length sequences from the genomic DNA of Solanum tuberosum genes encoding translation initiation factors of the eIF4E family, as well as for the synthesis of fragments of the potato Y virus genome from cDNA of potato plants infected by this virus. It was found that the efficiency of amplification by various DNA polymerases generally decreased with increasing length of the amplic

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Antipov, A. D., and N. E. Zlobin. "The Efficiency of Various DNA Polymerases for Amplification of Long Sequences from Genomic DNA and cDNA of Cultivated Potatoes." Applied Biochemistry and Microbiology 59, no. 4 (2023): 522–29. http://dx.doi.org/10.1134/s0003683823040026.

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Abstract Amplification of long fragments from complex templates, such as eukaryotic genomic DNA, is considered a difficult task for most DNA polymerases. In this research, six DNA polymerases were used to amplify full-length sequences from the genomic DNA of Solanum tuberosum genes encoding translation initiation factors of the eIF4E family, as well as for the synthesis of fragments of the potato Y virus genome from cDNA of potato plants infected by this virus. It was found that the efficiency of amplification by various DNA polymerases generally decreased with the increasing length of the amp

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Shareef, Afzaal M., Barbara Ludeke, Paul Jordan, Jerome Deval, and Rachel Fearns. "Comparison of RNA synthesis initiation properties of non-segmented negative strand RNA virus polymerases." PLOS Pathogens 17, no. 12 (2021): e1010151. http://dx.doi.org/10.1371/journal.ppat.1010151.

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It is generally thought that the promoters of non-segmented, negative strand RNA viruses (nsNSVs) direct the polymerase to initiate RNA synthesis exclusively opposite the 3´ terminal nucleotide of the genome RNA by a de novo (primer independent) initiation mechanism. However, recent studies have revealed that there is diversity between different nsNSVs with pneumovirus promoters directing the polymerase to initiate at positions 1 and 3 of the genome, and ebolavirus polymerases being able to initiate at position 2 on the template. Studies with other RNA viruses have shown that polymerases that

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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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Budd, M. E., and J. L. Campbell. "DNA polymerases delta and epsilon are required for chromosomal replication in Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 1 (1993): 496–505. http://dx.doi.org/10.1128/mcb.13.1.496-505.1993.

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Three DNA polymerases, alpha, delta, and epsilon are required for viability in Saccharomyces cerevisiae. We have investigated whether DNA polymerases epsilon and delta are required for DNA replication. Two temperature-sensitive mutations in the POL2 gene, encoding DNA polymerase epsilon, have been identified by using the plasmid shuffle technique. Alkaline sucrose gradient analysis of DNA synthesis products in the mutant strains shows that no chromosomal-size DNA is formed after shift of an asynchronous culture to the nonpermissive temperature. The only DNA synthesis observed is a reduced quan

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Budd, M. E., and J. L. Campbell. "DNA polymerases delta and epsilon are required for chromosomal replication in Saccharomyces cerevisiae." Molecular and Cellular Biology 13, no. 1 (1993): 496–505. http://dx.doi.org/10.1128/mcb.13.1.496.

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Three DNA polymerases, alpha, delta, and epsilon are required for viability in Saccharomyces cerevisiae. We have investigated whether DNA polymerases epsilon and delta are required for DNA replication. Two temperature-sensitive mutations in the POL2 gene, encoding DNA polymerase epsilon, have been identified by using the plasmid shuffle technique. Alkaline sucrose gradient analysis of DNA synthesis products in the mutant strains shows that no chromosomal-size DNA is formed after shift of an asynchronous culture to the nonpermissive temperature. The only DNA synthesis observed is a reduced quan

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Serrano, Alicia, Martín Moret, Isabel Fernández-Parras, Aureliano Bombarely, Francisco Luque, and Francisco Navarro. "RNA Polymerases IV and V Are Involved in Olive Fruit Development." Genes 15, no. 1 (2023): 1. http://dx.doi.org/10.3390/genes15010001.

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Transcription is carried out in most eukaryotes by three multimeric complexes (RNA polymerases I, II and III). However, plants contain two additional RNA polymerases (IV and V), which have evolved from RNA polymerase II. RNA polymerases II, IV and V contain both common and specific subunits that may specialise some of their functions. In this study, we conducted a search for the genes that putatively code for the specific subunits of RNA polymerases IV and V, as well as those corresponding to RNA polymerase II in olive trees. Based on the homology with the genes of Arabidopsis thaliana, we ide

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Lo, Chen-Yu, and Yang Gao. "DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication." International Journal of Molecular Sciences 23, no. 3 (2022): 1342. http://dx.doi.org/10.3390/ijms23031342.

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DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the p

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Niimi, Atsuko, Siripan Limsirichaikul, Shonen Yoshida та ін. "Palm Mutants in DNA Polymerases α and η Alter DNA Replication Fidelity and Translesion Activity". Molecular and Cellular Biology 24, № 7 (2004): 2734–46. http://dx.doi.org/10.1128/mcb.24.7.2734-2746.2004.

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ABSTRACT We isolated active mutants in Saccharomyces cerevisiae DNA polymerase α that were associated with a defect in error discrimination. Among them, L868F DNA polymerase α has a spontaneous error frequency of 3 in 100 nucleotides and 570-fold lower replication fidelity than wild-type (WT) polymerase α. In vivo, mutant DNA polymerases confer a mutator phenotype and are synergistic with msh2 or msh6, suggesting that DNA polymerase α-dependent replication errors are recognized and repaired by mismatch repair. In vitro, L868F DNA polymerase α catalyzes efficient bypass of a cis-syn cyclobutane

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Villarreal, Luis P., and Victor R. DeFilippis. "A Hypothesis for DNA Viruses as the Origin of Eukaryotic Replication Proteins." Journal of Virology 74, no. 15 (2000): 7079–84. http://dx.doi.org/10.1128/jvi.74.15.7079-7084.2000.

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ABSTRACT The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from phycodnavirus (which infects microalgae) as the basis of this analysis, as it represents a virus of a primitive eukaryote. We show that it has significant similarity with replicative DNA polymerases of eukaryotes and certain of their large DNA viruses. Sequence alignment confir

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