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Journal articles on the topic 'Uracil N-glycosylase'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 September 2023

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1

Focher, F., A. Verri, S. Spadari, R. Manservigi, J. Gambino, and G. E. Wright. "Herpes simplex virus type 1 uracil-DNA glycosylase: isolation and selective inhibition by novel uracil derivatives." Biochemical Journal 292, no. 3 (1993): 883–89. http://dx.doi.org/10.1042/bj2920883.

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We have purified Herpes simplex type 1 (HSV1) uracil-DNA glycosylase from the nuclei of HSV1-infected HeLa cells harvested 8 h post-infection, at which time the induction of the enzyme is a maximum. The enzyme has been shown to be distinct from the host enzyme, isolated from HeLa cells, by its lack of sensitivity to a monoclonal antibody to human uracil-DNA glycosylase. Furthermore, several uracil analogues were synthesized and screened for their capacity to discriminate between the viral and human uracil-DNA glycosylases. Both enzymes were inhibited by 6-(p-alkylanilino)uracils, but the viral

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2

SHATILLA, Andrea, and Dindial RAMOTAR. "Embryonic extracts derived from the nematode Caenorhabditis elegans remove uracil from DNA by the sequential action of uracil-DNA glycosylase and AP (apurinic/apyrimidinic) endonuclease." Biochemical Journal 365, no. 2 (2002): 547–53. http://dx.doi.org/10.1042/bj20020375.

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DNA bases continuously undergo modifications in response to endogenous reactions such as oxidation, alkylation or deamination. The modified bases are primarily removed by DNA glycosylases, which cleave the N-glycosylic bond linking the base to the sugar, to generate an apurinic/apyrimidinic (AP) site, and this latter lesion is highly mutagenic. Previously, no study has demonstrated the processing of these lesions in the nematode Caenorhabditis elegans. Herein, we report the existence of uracil-DNA glycosylase and AP endonuclease activities in extracts derived from embryos of C. elegans. These

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3

Di Noia, Javier M., Gareth T. Williams, Denice T. Y. Chan, Jean-Marie Buerstedde, Geoff S. Baldwin, and Michael S. Neuberger. "Dependence of antibody gene diversification on uracil excision." Journal of Experimental Medicine 204, no. 13 (2007): 3209–19. http://dx.doi.org/10.1084/jem.20071768.

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Activation-induced deaminase (AID) catalyses deamination of deoxycytidine to deoxyuridine within immunoglobulin loci, triggering pathways of antibody diversification that are largely dependent on uracil-DNA glycosylase (uracil-N-glycolase [UNG]). Surprisingly efficient class switch recombination is restored to ung−/− B cells through retroviral delivery of active-site mutants of UNG, stimulating discussion about the need for UNG's uracil-excision activity. In this study, however, we find that even with the overexpression achieved through retroviral delivery, switching is only mediated by UNG mu

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4

KROKAN, Hans E., Rune STANDAL, and Geir SLUPPHAUG. "DNA glycosylases in the base excision repair of DNA." Biochemical Journal 325, no. 1 (1997): 1–16. http://dx.doi.org/10.1042/bj3250001.

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A wide range of cytotoxic and mutagenic DNA bases are removed by different DNA glycosylases, which initiate the base excision repair pathway. DNA glycosylases cleave the N-glycosylic bond between the target base and deoxyribose, thus releasing a free base and leaving an apurinic/apyrimidinic (AP) site. In addition, several DNA glycosylases are bifunctional, since they also display a lyase activity that cleaves the phosphodiester backbone 3′ to the AP site generated by the glycosylase activity. Structural data and sequence comparisons have identified common features among many of the DNA glycos

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5

Loewy, Z. G., J. Mecca, and R. Diaco. "Enhancement of Borrelia burgdorferi PCR by uracil N-glycosylase." Journal of Clinical Microbiology 32, no. 1 (1994): 135–38. http://dx.doi.org/10.1128/jcm.32.1.135-138.1994.

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6

Kavli, Bodil, Tobias S. Iveland, Edith Buchinger, et al. "RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork." Nucleic Acids Research 49, no. 7 (2021): 3948–66. http://dx.doi.org/10.1093/nar/gkab195.

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Abstract Uracil occurs at replication forks via misincorporation of deoxyuridine monophosphate (dUMP) or via deamination of existing cytosines, which occurs 2–3 orders of magnitude faster in ssDNA than in dsDNA and is 100% miscoding. Tethering of UNG2 to proliferating cell nuclear antigen (PCNA) allows rapid post-replicative removal of misincorporated uracil, but potential ‘pre-replicative’ removal of deaminated cytosines in ssDNA has been questioned since this could mediate mutagenic translesion synthesis and induction of double-strand breaks. Here, we demonstrate that uracil-DNA glycosylase

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7

Prorok, Paulina, Inga R. Grin, Bakhyt T. Matkarimov, et al. "Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases." Cells 10, no. 7 (2021): 1591. http://dx.doi.org/10.3390/cells10071591.

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It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites an

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8

Delbos, Frédéric, Said Aoufouchi, Ahmad Faili, Jean-Claude Weill та Claude-Agnès Reynaud. "DNA polymerase η is the sole contributor of A/T modifications during immunoglobulin gene hypermutation in the mouse". Journal of Experimental Medicine 204, № 1 (2006): 17–23. http://dx.doi.org/10.1084/jem.20062131.

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Mutations at A/T bases within immunoglobulin genes have been shown to be generated by a repair pathway involving the DNA-binding moiety of the mismatch repair complex constituted by the MSH2–MSH6 proteins, together with DNA polymerase η (pol η). However, residual A/T mutagenesis is still observed upon inactivation in the mouse of each of these factors, suggesting that the panel of activities involved might be more complex. We reported previously (Delbos, F., A. De Smet, A. Faili, S. Aoufouchi, J.-C. Weill, and C.-A. Reynaud. 2005. J. Exp. Med. 201:1191–1196) that residual A/T mutagenesis in po

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9

Wynn, Emily, Emma Purfeerst, and Alan Christensen. "Mitochondrial DNA Repair in an Arabidopsis thaliana Uracil N-Glycosylase Mutant." Plants 9, no. 2 (2020): 261. http://dx.doi.org/10.3390/plants9020261.

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Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determi

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10

Zeitlin, Samantha G., Brian R. Chapados, Norman M. Baker, Caroline Tai, Geir Slupphaug, and Jean Y. J. Wang. "Uracil DNA N-Glycosylase Promotes Assembly of Human Centromere Protein A." PLoS ONE 6, no. 3 (2011): e17151. http://dx.doi.org/10.1371/journal.pone.0017151.

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11

Weiser, Brian P., Gaddiel Rodriguez, Alexandre Esadze, Philip A. Cole, and James T. Stivers. "Function of the Intrinsically Disordered N-Terminus of Uracil DNA Glycosylase." Biophysical Journal 114, no. 3 (2018): 82a. http://dx.doi.org/10.1016/j.bpj.2017.11.494.

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12

Lu, Chih-Chung, Ho-Ting Huang, Jiin-Tarng Wang, et al. "Characterization of the Uracil-DNA Glycosylase Activity of Epstein-Barr Virus BKRF3 and Its Role in Lytic Viral DNA Replication." Journal of Virology 81, no. 3 (2006): 1195–208. http://dx.doi.org/10.1128/jvi.01518-06.

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ABSTRACT Uracil-DNA glycosylases (UDGs) of the uracil-N-glycosylase (UNG) family are the primary DNA repair enzymes responsible for removal of inappropriate uracil from DNA. Recent studies further suggest that the nuclear human UNG2 and the UDGs of large DNA viruses may coordinate with their DNA polymerase accessory factors to enhance DNA replication. Based on its amino acid sequence, the putative UDG of Epstein-Barr virus (EBV), BKRF3, belongs to the UNG family of proteins, and it was demonstrated previously to enhance oriLyt-dependent DNA replication in a cotransfection replication assay. Ho

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13

Perkins, Jacob L., and Linlin Zhao. "The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions." DNA Repair 101 (May 2021): 103077. http://dx.doi.org/10.1016/j.dnarep.2021.103077.

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14

Pedersen, Hege Lynum, Kenneth A. Johnson, Colin E. McVey, Ingar Leiros, and Elin Moe. "Structure determination of uracil-DNAN-glycosylase fromDeinococcus radioduransin complex with DNA." Acta Crystallographica Section D Biological Crystallography 71, no. 10 (2015): 2137–49. http://dx.doi.org/10.1107/s1399004715014157.

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Uracil-DNAN-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacteriumDeinococcus radiodurans(DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity betweenDrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well

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15

Renganathan, Senthil, Subrata Pramanik, Rajasekaran Ekambaram, Arne Kutzner, Pok-Son Kim, and Klaus Heese. "Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing." Cancers 13, no. 22 (2021): 5870. http://dx.doi.org/10.3390/cancers13225870.

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Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2, the enzyme that prevents mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a mole

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16

Diatlova, Evgeniia A., Grigory V. Mechetin, Anna V. Yudkina, et al. "Correlated Target Search by Vaccinia Virus Uracil–DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery." International Journal of Molecular Sciences 24, no. 11 (2023): 9113. http://dx.doi.org/10.3390/ijms24119113.

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The protein encoded by the vaccinia virus D4R gene has base excision repair uracil–DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG al

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17

Rodriguez, Gaddiel, Alexandre Esadze, Brian P. Weiser, Joseph D. Schonhoft, Philip A. Cole, and James T. Stivers. "Disordered N-Terminal Domain of Human Uracil DNA Glycosylase (hUNG2) Enhances DNA Translocation." ACS Chemical Biology 12, no. 9 (2017): 2260–63. http://dx.doi.org/10.1021/acschembio.7b00521.

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18

Weiser, Brian P., James T. Stivers, and Philip A. Cole. "Investigation of N-Terminal Phospho-Regulation of Uracil DNA Glycosylase Using Protein Semisynthesis." Biophysical Journal 113, no. 2 (2017): 393–401. http://dx.doi.org/10.1016/j.bpj.2017.06.016.

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19

Weiser, Brian P., Gaddiel Rodriguez, Philip A. Cole, and James T. Stivers. "N-terminal domain of human uracil DNA glycosylase (hUNG2) promotes targeting to uracil sites adjacent to ssDNA–dsDNA junctions." Nucleic Acids Research 46, no. 14 (2018): 7169–78. http://dx.doi.org/10.1093/nar/gky525.

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20

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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21

Ball, Jonathan K., and Ulrich Desselberger. "The use of uracil-N-glycosylase in the preparation of PCR products of direct sequencing." Nucleic Acids Research 20, no. 12 (1992): 3255. http://dx.doi.org/10.1093/nar/20.12.3255.

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22

Durandy, Anne. "Immunoglobulin class switch recombination: study through human natural mutants." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1517 (2008): 577–82. http://dx.doi.org/10.1098/rstb.2008.0210.

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Immunoglobulin class switch recombination deficiencies in humans are exquisite models to analyse the mechanisms of class switch recombination (CSR). Besides defects in CD40L/CD40 interaction, others result from an intrinsic B-cell deficiency. The recent elucidation of the molecular basis of some of them has made it possible to delineate the molecular events involved in antibody maturation. Activation-induced (cytidine) deaminase (AID) and uracil-N-glycosylase deficiencies have demonstrated the role of AID as the inducer of DNA lesions in switch and variable regions. However, most of these CSR

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23

Saparbaev, Murat, Sophie Langouët, Cyril V. Privezentzev, et al. "1,N2-Ethenoguanine, a Mutagenic DNA Adduct, Is a Primary Substrate ofEscherichia coliMismatch-specific Uracil-DNA Glycosylase and Human Alkylpurine-DNA-N-Glycosylase." Journal of Biological Chemistry 277, no. 30 (2002): 26987–93. http://dx.doi.org/10.1074/jbc.m111100200.

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24

Ræder, Inger Lin Uttakleiv, Ingar Leiros, Nils Peder Willassen, Arne O. Smalås, and Elin Moe. "Uracil-DNA N-glycosylase (UNG) from the marine, psychrophilic bacterium Vibrio salmonicida shows cold adapted features." Enzyme and Microbial Technology 42, no. 7 (2008): 594–600. http://dx.doi.org/10.1016/j.enzmictec.2008.02.005.

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25

Dizdaroglu, M., A. Karakaya, P. Jaruga, G. Slupphaug, and H. E. Krokan. "Novel Activities of Human Uracil DNA N-Glycosylase for Cytosine-Derived Products of Oxidative DNA Damage." Nucleic Acids Research 24, no. 3 (1996): 418–22. http://dx.doi.org/10.1093/nar/24.3.418.

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26

Ball, Jonathan K., and Rebecca Curran. "Production of Single-Stranded DNA Using a Uracil-N-glycosylase-Mediated Asymmetric Polymerase Chain Reaction Method." Analytical Biochemistry 253, no. 2 (1997): 264–67. http://dx.doi.org/10.1006/abio.1997.2348.

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27

Andersson, Daniel, David Svec, Cathrine Pedersen, Jørn Henriksen, and Anders Ståhlberg. "Preamplification with dUTP and Cod UNG Enables Elimination of Contaminating Amplicons." International Journal of Molecular Sciences 19, no. 10 (2018): 3185. http://dx.doi.org/10.3390/ijms19103185.

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Analyzing rare DNA and RNA molecules in limited sample sizes, such as liquid biopsies and single cells, often requires preamplification, which makes downstream analyses particularly sensitive to polymerase chain reaction (PCR) generated contamination. Herein, we assessed the feasibility of performing Cod uracil-DNA N-glycosylase (Cod UNG) treatment in combination with targeted preamplification, using deoxyuridine triphosphate (dUTP) to eliminate carry-over DNA. Cod UNG can be completely and irreversibly heat inactivated, a prerequisite in preamplification methods, where any loss of amplicons i

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28

Purmal, A. A., G. W. Lampman, E. I. Pourmal, R. J. Melamede, S. S. Wallace, and Y. W. Kow. "Uracil DNA N-glycosylase distributively interacts with duplex polynucleotides containing repeating units of either TGGCCAAGCU or TGGCCAAGCTTGGCCAAGCU." Journal of Biological Chemistry 269, no. 35 (1994): 22046–53. http://dx.doi.org/10.1016/s0021-9258(17)31753-2.

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29

Péron, Sophie, Ayse Metin, Pauline Gardès, et al. "Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination." Journal of Experimental Medicine 205, no. 11 (2008): 2465–72. http://dx.doi.org/10.1084/jem.20080789.

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Immunoglobulin (Ig) class switch recombination (CSR) deficiencies are rare primary immunodeficiencies characterized by the lack of switched isotype (IgG/IgA/IgE) production. In some cases, CSR deficiencies can be associated with abnormal somatic hypermutation. Analysis of CSR deficiencies has helped reveal the key functions of CSR-triggering molecules, i.e., CD40L, CD40, and effector molecules such as activation-induced cytidine deaminase and uracil N-glycosylase. We report a new form of B cell–intrinsic CSR deficiency found in three patients with deleterious, homozygous mutations in the gene

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30

Argnani, R., F. Focher, S. Zucchini, et al. "Herpes Simplex Virus Type 1 (HSV-1) Uracil-DNA Glycosylase: Functional Expression in Escherichia coli, Biochemical Characterization, and Selective Inhibition by 6-(p-n-Octylanilino)Uracil." Virology 211, no. 1 (1995): 307–11. http://dx.doi.org/10.1006/viro.1995.1406.

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31

Péron, Sophie, Qiang Pan-Hammarström, Kohsuke Imai, et al. "A primary immunodeficiency characterized by defective immunoglobulin class switch recombination and impaired DNA repair." Journal of Experimental Medicine 204, no. 5 (2007): 1207–16. http://dx.doi.org/10.1084/jem.20070087.

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Immunoglobulin class switch recombination (CSR) deficiencies are rare primary immunodeficiencies, characterized by a lack of switched isotype (IgG, IgA, or IgE) production, variably associated with abnormal somatic hypermutation (SHM). Deficiencies in CD40 ligand, CD40, activation-induced cytidine deaminase, and uracil-N-glycosylase may account for this syndrome. We previously described another Ig CSR deficiency condition, characterized by a defect in CSR downstream of the generation of double-stranded DNA breaks in switch (S) μ regions. Further analysis performed with the cells of five affect

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32

Nelson, Joshua H., Gregory A. Hawkins, Karin Edlund, et al. "A Novel and Rapid PCR-Based Method for Genotyping Human Papillomaviruses in Clinical Samples." Journal of Clinical Microbiology 38, no. 2 (2000): 688–95. http://dx.doi.org/10.1128/jcm.38.2.688-695.2000.

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Many human papillomavirus (HPV) genotypes are associated with cervical carcinoma. We demonstrate the utility of an innovative technique for genotyping of HPV in cervical tissue samples. This method provides an accurate means of identification of the specific HPV genotypes present in clinical specimens. By using the MY09-MY11 and the GP5+-GP6+ consensus primer pairs, HPV sequences were amplified by nested PCR from DNA isolated from cervical smear samples. This led to the production of an approximately 140-bp PCR product from the L1 (major capsid) gene of any of the HPVs present in the sample. P

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33

Gobet, P., J. C. Buisson, O. Vagner, et al. "Detection of Cryptosporidium parvum DNA in formed human feces by a sensitive PCR-based assay including uracil-N-glycosylase inactivation." Journal of clinical microbiology 35, no. 1 (1997): 254–56. http://dx.doi.org/10.1128/jcm.35.1.254-256.1997.

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34

Pérez-Durán, Pablo, Laura Belver, Virginia G. de Yébenes, Pilar Delgado, David G. Pisano, and Almudena R. Ramiro. "UNG shapes the specificity of AID-induced somatic hypermutation." Journal of Experimental Medicine 209, no. 7 (2012): 1379–89. http://dx.doi.org/10.1084/jem.20112253.

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Secondary diversification of antibodies through somatic hypermutation (SHM) and class switch recombination (CSR) is a critical component of the immune response. Activation-induced deaminase (AID) initiates both processes by deaminating cytosine residues in immunoglobulin genes. The resulting U:G mismatch can be processed by alternative pathways to give rise to a mutation (SHM) or a DNA double-strand break (CSR). Central to this processing is the activity of uracil-N-glycosylase (UNG), an enzyme normally involved in error-free base excision repair. We used next generation sequencing to analyze

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35

Nakura, Yukiko, Heng Ning Wu, Yuya Okamoto, et al. "Development of an efficient one-step real-time reverse transcription polymerase chain reaction method for severe acute respiratory syndrome-coronavirus-2 detection." PLOS ONE 16, no. 6 (2021): e0252789. http://dx.doi.org/10.1371/journal.pone.0252789.

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The general methods to detect the RNA of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in clinical diagnostic testing involve reverse transcriptases and thermostable DNA polymerases. In this study, we compared the detection of SARS-CoV-2 by a one-step real-time RT-PCR method using a heat-resistant reverse transcriptase variant MM4 from Moloney murine leukemia virus, two thermostable DNA polymerase variants with reverse transcriptase activity from Thermotoga petrophila K4 and Thermococcus kodakarensis KOD1, or a wild-type DNA polymerase from Thermus thermophilus M1. The highest p

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36

Moe, Elin, Ingar Leiros, Ellen Kristin Riise, et al. "Optimisation of the Surface Electrostatics as a Strategy for Cold Adaptation of Uracil-DNA N-glycosylase (UNG) from Atlantic Cod (Gadus morhua)." Journal of Molecular Biology 343, no. 5 (2004): 1221–30. http://dx.doi.org/10.1016/j.jmb.2004.09.004.

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37

Poddar, Saibal K., Mark H. Sawyer, and James D. Connor. "Optimized PCR amplification of influenza A virus RNA using Tth DNA polymerase, incorporating uracil N glycosylase (UNG) in a single tube reaction." Journal of Clinical Laboratory Analysis 11, no. 6 (1997): 323–27. http://dx.doi.org/10.1002/(sici)1098-2825(1997)11:6<323::aid-jcla2>3.0.co;2-6.

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38

Assefa, Netsanet Gizaw, Laila Niiranen, Nils Peder Willassen, Arne Smalås, and Elin Moe. "Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG." Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 161, no. 1 (2012): 60–68. http://dx.doi.org/10.1016/j.cbpb.2011.09.007.

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39

Ye, Feng, Hanzhi Wang, Jia Liu, Qi Cheng, Xiaojing Chen, and Huaizeng Chen. "Genetic polymorphism (rs246079) of the DNA repair gene uracil N-glycosylase is associated with increased risk of cervical carcinoma in a Chinese population." Medicine 97, no. 51 (2018): e13694. http://dx.doi.org/10.1097/md.0000000000013694.

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40

Hatahet, Z., Y. W. Kow, A. A. Purmal, R. P. Cunningham, and S. S. Wallace. "New substrates for old enzymes. 5-Hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2'-deoxyuridine is a substrate for uracil DNA N-glycosylase." Journal of Biological Chemistry 269, no. 29 (1994): 18814–20. http://dx.doi.org/10.1016/s0021-9258(17)32239-1.

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41

Zeng, Dongchang, Zhiye Zheng, Yuxin Liu, et al. "Exploring C-to-G and A-to-Y Base Editing in Rice by Using New Vector Tools." International Journal of Molecular Sciences 23, no. 14 (2022): 7990. http://dx.doi.org/10.3390/ijms23147990.

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CRISPR/Cas9-based cytosine base editors (CBEs) and adenine base editors (ABEs) can efficiently mediate C-to-T/G-to-A and A-to-G/T-to-C substitutions, respectively; however, achieving base transversions (C-to-G/C-to-A and A-to-T/A-to-C) is challenging and has been rarely studied in plants. Here, we constructed new plant C-to-G base editors (CGBEs) and new A-to-Y (T/C) base editors and explored their base editing characteristics in rice. First, we fused the highly active cytidine deaminase evoFENRY and the PAM-relaxed Cas9-nickase variant Cas9n-NG with rice and human uracil DNA N-glycosylase (rU

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42

King, Julie A., and Jonathan K. Ball. "Detection of HIV-1 by digoxigenin-labelled PCR and microtitre plate solution hybridisation assay and prevention of PCR carry-over by uracil-N-glycosylase." Journal of Virological Methods 44, no. 1 (1993): 67–76. http://dx.doi.org/10.1016/0166-0934(93)90008-f.

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Josefsson, Agnetha, Ken Livak, and Ulf Gyllensten. "Detection and Quantitation of Human Papillomavirus by Using the Fluorescent 5′ Exonuclease Assay." Journal of Clinical Microbiology 37, no. 3 (1999): 490–96. http://dx.doi.org/10.1128/jcm.37.3.490-496.1999.

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A method for the detection and quantitation of oncogenic human papillomavirus (HPV) was developed by using the fluorescent 5′ exonuclease assay. The method is based on the amplification of a 180-bp fragment from the 3′ part of the E1 open reading frame in a single PCR with type-specific probes for HPV types 16, 18, 31, 33, and 35. The probes can be used separately or in combinations of up to three probes per assay. Quantitation over a range of 101 to 106 initial HPV copies was possible by using real-time detection of the accumulation of fluorescence with cycle number. Reconstitution experiment

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Zastawny, Tomasz H., Paul W. Doetsch, and Miral Dizdaroglu. "A novel activity of E. coli uracil DNA N -glycosylase excision of isodialuric acid (5,6-dihydroxyuracil), a major product of oxidative DNA damage, from DNA." FEBS Letters 364, no. 3 (1995): 255–58. http://dx.doi.org/10.1016/0014-5793(95)00400-4.

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Schwab, K. J., F. H. Neill, M. K. Estes, and R. L. Atmar. "Improvements in the RT-PCR detection of enteric viruses in environmental samples." Water Science and Technology 38, no. 12 (1998): 83–86. http://dx.doi.org/10.2166/wst.1998.0508.

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Current methods for the detection of nucleic acid from enteric viruses in environmental samples usually involve extensive concentration and purification of target viruses followed by RT-PCR amplification using two enzymes, reverse transcriptase and Taq polymerase. We have developed a modified method that improves RT-PCR assays by: (i) the use of an RT-PCR internal standard control RNA to identify potential false negative results caused by inhibition of RT-PCR enzymes; (ii) the use of rTth (Perkin-Elmer, Foster City, CA), a heat-stable enzyme that functions as both a reverse transcriptase and D

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Schwab, Kellogg J., Frederick H. Neill, Françoise Le Guyader, Mary K. Estes, and Robert L. Atmar. "Development of a Reverse Transcription-PCR–DNA Enzyme Immunoassay for Detection of “Norwalk-Like” Viruses and Hepatitis A Virus in Stool and Shellfish." Applied and Environmental Microbiology 67, no. 2 (2001): 742–49. http://dx.doi.org/10.1128/aem.67.2.742-749.2001.

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ABSTRACT Outbreaks of food- and waterborne gastroenteritis are being increasingly reported throughout the world. The analysis of environmental samples by newer diagnostic techniques such as reverse transcription-PCR (RT-PCR) amplification of nucleic acid has begun to identify human enteric viruses (predominantly “Norwalk-like” viruses [NLVs]) as the cause of many of these outbreaks. To streamline NLV detection from environmental samples such as shellfish, we have developed an RT-PCR–oligoprobe amplification and detection method using several new procedures that enable confirmed RT-PCR amplific

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Yamamoto, Shin, Katsuhide Miyake, Yoichi Koike, et al. "Molecular Characterization of Type-Specific Capsular Polysaccharide Biosynthesis Genes of Streptococcus agalactiae Type Ia." Journal of Bacteriology 181, no. 17 (1999): 5176–84. http://dx.doi.org/10.1128/jb.181.17.5176-5184.1999.

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ABSTRACT The type-specific capsular polysaccharide (CP) of a group B streptococcus, Streptococcus agalactiae type Ia, is a high-molecular-weight polymer consisting of the pentasaccharide repeating unit 4)-[α-d-NeupNAc-(2→3)-β-d-Galp-(1→4)-β-d-GlcpNAc-(1→3)]-β-d-Galp-(1→4)-β-d-Glcp-(1. Here, cloning, sequencing, and transcription of the type Ia-specific capsular polysaccharide synthesis (cps) genes and functional analysis of these gene products are described. A 26-kb DNA fragment containing 18 complete open reading frames (ORFs) was cloned. These ORFs were designated cpsIaA tocpsIaL, neu (neura

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Schwab, Kellogg J., and James J. McDevitt. "Development of a PCR-Enzyme Immunoassay Oligoprobe Detection Method for Toxoplasma gondii Oocysts, Incorporating PCR Controls." Applied and Environmental Microbiology 69, no. 10 (2003): 5819–25. http://dx.doi.org/10.1128/aem.69.10.5819-5825.2003.

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ABSTRACT Infections caused by Toxoplasma gondii are widely prevalent in animals and humans throughout the world. In the United States, an estimated 23% of adolescents and adults have laboratory evidence of T. gondii infection. T. gondii has been identified as a major opportunistic pathogen in immunocompromised individuals, in whom it can cause life-threatening disease. Water contaminated with feces from domestic cats or other felids may be an important source of human exposure to T. gondii oocysts. Because of the lack of information regarding the prevalence of T. gondii in surface waters, ther

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Filisetti, Denis, Yvon Sterkers, Marie-Pierre Brenier-Pinchart, et al. "Multicentric Comparative Assessment of the Bio-Evolution Toxoplasma gondii Detection Kit with Eight Laboratory-Developed PCR Assays for Molecular Diagnosis of Congenital Toxoplasmosis." Journal of Clinical Microbiology 53, no. 1 (2014): 29–34. http://dx.doi.org/10.1128/jcm.01913-14.

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The detection ofToxoplasma gondiiin amniotic fluid is an essential tool for the prenatal diagnosis of congenital toxoplasmosis and is currently essentially based on the use of PCR. Although some consensus is emerging, this molecular diagnosis suffers from a lack of standardization and an extreme diversity of laboratory-developed methods. Commercial kits for the detection ofT. gondiiby PCR were recently developed and offer certain advantages; however, they must be assessed in comparison with optimized reference PCR assays. The present multicentric study aimed to compare the performances of the

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Lee, Hyeon Cheol, Jin Ha Kim, Jin Sook Kim, Wonhee Jang, and Sang Yong Kim. "Fermentative Production of Thymidine by a Metabolically Engineered Escherichia coli Strain." Applied and Environmental Microbiology 75, no. 8 (2009): 2423–32. http://dx.doi.org/10.1128/aem.02328-08.

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ABSTRACT Thymidine is an important precursor in the production of various antiviral drugs, including azidothymidine for the treatment of AIDS. Since thymidine-containing nucleotides are synthesized only by the de novo pathway during DNA synthesis, it is not easy to produce a large amount of thymidine biologically. In order to develop a host strain to produce thymidine, thymidine phosphorylase, thymidine kinase, and uridine phosphorylase genes were deleted from an Escherichia coli BL21 strain to develop BLdtu. Since the genes coding for the enzymes related to the nucleotide salvage pathway were

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