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| ???org.dspace.app.webui.jsptag.ItemTag.dcfield??? | Value | Language |
|---|---|---|
| dc.contributor.advisor | 方偉宏 | |
| dc.contributor.author | Wei-Chen Chang | en |
| dc.contributor.author | 張煒晨 | zh_TW |
| dc.date.accessioned | 2021-06-16T09:17:59Z | - |
| dc.date.available | 2017-09-12 | |
| dc.date.copyright | 2017-09-12 | |
| dc.date.issued | 2017 | |
| dc.date.submitted | 2017-07-11 | |
| dc.identifier.citation | Brutlag, D., & Kornberg, A. (1972). Enzymatic synthesis of deoxyribonucleic acid. 36. A proofreading function for the 3' leads to 5' exonuclease activity in deoxyribonucleic acid polymerases. J Biol Chem, 247(1), 241-248.
Cao, W. (2013). Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell Mol Life Sci, 70(17), 3145-3156. doi:10.1007/s00018-012-1222-z Cowart, M., Gibson, K. J., Allen, D. J., & Benkovic, S. J. (1989). DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry, 28(5), 1975-1983. Dalhus, B., Arvai, A. S., Rosnes, I., Olsen, O. E., Backe, P. H., Alseth, I., . . . Bjoras, M. (2009). Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol, 16(2), 138-143. doi:10.1038/nsmb.1538 Drake, J. W. (1991). A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A, 88(16), 7160-7164. Fang, W., Wu, J. Y., & Su, M. J. (1997). Methyl-directed repair of mismatched small heterologous sequences in cell extracts from Escherichia coli. J Biol Chem, 272(36), 22714-22720. Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. 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Kawase, Y., Iwai, S., Inoue, H., Miura, K., & Ohtsuka, E. (1986). Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases. Nucleic Acids Res, 14(19), 7727-7736. Klenow, H., & Henningsen, I. (1970). Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc Natl Acad Sci U S A, 65(1), 168-175. Kunkel, T. A., & Bebenek, K. (2000). DNA replication fidelity. Annu Rev Biochem, 69, 497-529. doi:10.1146/annurev.biochem.69.1.497 Lahue, R. S., Au, K. G., & Modrich, P. (1989). DNA mismatch correction in a defined system. Science, 245(4914), 160-164. Lee, C. C., Yang, Y. C., Goodman, S. D., Lin, C. J., Chen, Y. A., Wang, Y. T., Fang, W. H. (2013). The excision of 3' penultimate errors by DNA polymerase I and its role in endonuclease V-mediated DNA repair. DNA Repair (Amst), 12(11), 899-911. doi:10.1016/j.dnarep.2013.08.003 Lee, C. C., Yang, Y. C., Goodman, S. D., Yu, Y. H., Lin, S. B., Kao, J. T., .Fang, W. H. (2010). Endonuclease V-mediated deoxyinosine excision repair in vitro. DNA Repair (Amst), 9(10), 1073-1079. doi:10.1016/j.dnarep.2010.07.007 Lehman, I. R., Bessman, M. J., Simms, E. S., & Kornberg, A. (1958). Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem, 233(1), 163-170. Lehman, I. R., & Chien, J. R. (1973). Persistence of deoxyribonucleic acid polymerase I and its 5'--3' exonuclease activity in PolA mutants of Escherichia coli K12. J Biol Chem, 248(22), 7717-7723. Lindahl, T., & Wood, R. D. (1999). Quality control by DNA repair. Science, 286(5446), 1897-1905. Loft, S., & Poulsen, H. E. (1996). Cancer risk and oxidative DNA damage in man. J Mol Med (Berl), 74(6), 297-312. Lucas, L. T., Gatehouse, D., & Shuker, D. E. (1999). Efficient nitroso group transfer from N-nitrosoindoles to nucleotides and 2'-deoxyguanosine at physiological pH. A new pathway for N-nitrosocompounds to exert genotoxicity. J Biol Chem, 274(26), 18319-18326. Madzak, C., Menck, C. F., Armier, J., & Sarasin, A. (1989). Analysis of single-stranded DNA stability and damage-induced strand loss in mammalian cells using SV40-based shuttle vectors. J Mol Biol, 205(3), 501-509. Martin, F. H., Castro, M. M., Aboul-ela, F., & Tinoco, I., Jr. (1985). Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res, 13(24), 8927-8938. Memisoglu, A., & Samson, L. (2000). Base excision repair in yeast and mammals. Mutat Res, 451(1-2), 39-51. Modrich, P. (1991). Mechanisms and biological effects of mismatch repair. Annu Rev Genet, 25, 229-253. doi:10.1146/annurev.ge.25.120191.001305 Moe, A., Ringvoll, J., Nordstrand, L. M., Eide, L., Bjoras, M., Seeberg, E., . . . Klungland, A. (2003). Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V. Nucleic Acids Res, 31(14), 3893-3900. Myrnes, B., Guddal, P. H., & Krokan, H. (1982). Metabolism of dITP in HeLa cell extracts, incorporation into DNA by isolated nuclei and release of hypoxanthine from DNA by a hypoxanthine-DNA glycosylase activity. Nucleic Acids Res, 10(12), 3693-3701. Napolitano, R., Janel-Bintz, R., Wagner, J., & Fuchs, R. P. (2000). All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J, 19(22), 6259-6265. doi:10.1093/emboj/19.22.6259 Nusslein, V., Otto, B., Bonhoeffer, F., & Schaller, H. (1971). Function of DNA polymerase 3 in DNA replication. Nat New Biol, 234(52), 285-286. Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., & Steitz, T. A. (1985). Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature, 313(6005), 762-766. Sancar, A. (1996). DNA excision repair. Annu Rev Biochem, 65, 43-81. doi:10.1146/annurev.bi.65.070196.000355 Saparbaev, M., Kleibl, K., & Laval, J. (1995). Escherichia coli, Saccharomyces cerevisiae, rat and human 3-methyladenine DNA glycosylases repair 1,N6-ethenoadenine when present in DNA. Nucleic Acids Res, 23(18), 3750-3755. Saparbaev, M., Mani, J. C., & Laval, J. (2000). Interactions of the human, rat, Saccharomyces cerevisiae and Escherichia coli 3-methyladenine-DNA glycosylases with DNA containing dIMP residues. Nucleic Acids Res, 28(6), 1332-1339. Schaaper, R. M. (1993). Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J Biol Chem, 268(32), 23762-23765. Schouten, K. A., & Weiss, B. (1999). Endonuclease V protects Escherichia coli against specific mutations caused by nitrous acid. Mutat Res, 435(3), 245-254. Shapiro, R., & Pohl, S. H. (1968). The reaction of ribonucleosides with nitrous acid. Side products and kinetics. Biochemistry, 7(1), 448-455. Sidorkina, O., Saparbaev, M., & Laval, J. (1997). Effects of nitrous acid treatment on the survival and mutagenesis of Escherichia coli cells lacking base excision repair (hypoxanthine-DNA glycosylase-ALK A protein) and/or nucleotide excision repair. Mutagenesis, 12(1), 23-28. Su, S. S., Lahue, R. S., Au, K. G., & Modrich, P. (1988). Mispair specificity of methyl-directed DNA mismatch correction in vitro. J Biol Chem, 263(14), 6829-6835. Van Houten, B. (1990). Nucleotide excision repair in Escherichia coli. Microbiol Rev, 54(1), 18-51. Watkins, N. E., Jr., & SantaLucia, J., Jr. (2005). Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res, 33(19), 6258-6267. doi:10.1093/nar/gki918 Weiss, B. (2008). Removal of deoxyinosine from the Escherichia coli chromosome as studied by oligonucleotide transformation. DNA Repair (Amst), 7(2), 205-212. doi:10.1016/j.dnarep.2007.09.010 Yao, M., Hatahet, Z., Melamede, R. J., & Kow, Y. W. (1994). Purification and characterization of a novel deoxyinosine-specific enzyme, deoxyinosine 3' endonuclease, from Escherichia coli. J Biol Chem, 269(23), 16260-16268. Yao, M., & Kow, Y. W. (1995). Interaction of deoxyinosine 3'-endonuclease from Escherichia coli with DNA containing deoxyinosine. J Biol Chem, 270(48), 28609-28616. Yao, M., & Kow, Y. W. (1996). Cleavage of insertion/deletion mismatches, flap and pseudo-Y DNA structures by deoxyinosine 3'-endonuclease from Escherichia coli. J Biol Chem, 271(48), 30672-30676. 尤詠絮 (2009) 亞黃嘌呤核酸鹼基切除修復試管中測定系統之研發 黎羿鈴 (2014) 第五型核酸內切酶及第一型核酸聚合酶校正外切酶處理亞硝酸傷害之生物學意義 鄧宇捷 (2014) 以質體為基礎之活體內DNA修復試驗研究 吳佩蓉 (2014) 核酸內切酶第五型主導之修復系統於生物體內亞黃嘌呤核酸修復之分析 吳卓遠 (2017) 細菌第一型DNA聚合酶校對外切酶參與第五型核酸內切酶修復之體內證明 | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59213 | - |
| dc.description.abstract | 細胞中的腺嘌呤(Adenine; A)會因發生自發性的脫胺作用或受到外源性的氧化壓力等傷害而變成次黃嘌呤(Hypoxanthine; Hx)。以Hx為鹼基與五碳醣結合，則稱為次黃嘌呤核苷酸(Deoxyinosine；dI)。第五型核酸內切酶修復系統(Endonuclease V repair pathway)是大腸桿菌中主要修復次黃嘌呤核苷酸的修復途徑之一。本實驗室先前已做過試管內次黃嘌呤核苷酸修復實驗，得知只需要第五型核酸內切酶、第一型DNA聚合酶、DNA連接酶即可完成整個修復反應。
我們希望能以細胞體內修復試驗印證此路徑，但本實驗室先前分別以噬菌體(M13mp18)以及質體(pUC18)作為載體所設計的T-I 核酸受質在進行細菌體內試驗時效果皆不理想。 因此本研究選擇使用噬菌粒(pBluescript II SK)作為載體，製備含T-I mismatch的核酸受質，期望此全新設計的核酸受質可同時適用於試管中以及細菌體內修復試驗，將此核酸受質分別轉型到BW25113 (WT)、JW5547 (nfi-) 、KA796 (polA+)、KA796 D424A (polA exo-)，四株不同的大腸桿菌中，進行細菌體內修復試驗。結果可看出JW5547 (nfi-)之修復效率較其野生株大腸桿菌低，而KA796 D424A (polA exo-)之修復效率和其野生株大腸桿菌相比並無差別，這和先前以質體為載體做出的偽陽性修復現象是相符的，我們懷疑是第五型核酸內切酶造成DNA缺口後，第一型DNA聚合酶大次單元無法移除錯誤片段完成修復，進而使DNA複製叉崩壞所造成的現象，因此我們無法判定核酸受質有無被修復成功，我們稱為偽陽性修復現象，因此本實驗室同時使用以噬菌粒作為載體之核酸受質，多設計一個C-C錯誤配對之標記，以區別偽陽性修復與陽性修復。 此外，本研究亦使用以噬菌粒作為載體之T-I核酸受質進行試管中純化蛋白質系統試驗，結果顯示在缺乏第一型核酸聚合酶中的3’-5’核酸外切酶活性的組別，其修復效率相較其他組別有明顯下降，證明了本實驗室對於第五型核酸內切酶修復系統路徑的推論，主要由第一型核酸聚合酶中3’-5’核酸外切酶的活性負責移除含有dI片段核酸。 | zh_TW |
| dc.description.abstract | The highly mutagenic deoxyinosine (dI) lesion can be produced in DNA spontaneously, and is enhanced by nitrous ion exposure. In Escherichia coli, dI is repaired through endonuclease V (EndoV) repair pathway. Our previous in vitro assay demonstrated that EndoV, DNA polymerase I (Pol I), and E. coli DNA ligase was sufficient to reconstitute the dI repair.
To find out gene products requirement for Endo V repair pathway, we employed both bacteriophage-based (M13mp18) dI-containing substrate and plasmid-based (pUC18) dI-containing substrate for in vivo repair assay. However, the results of both approaches were unsatisfactory. In this study, we developed a phagemid-based new substrate containing a T-I mismatch that can be used in both in vivo assay and in vitro assay. The results of T-I mismatch substrate demonstrated the similar repair level as in previous plasmid-based dI-containing substrate study: the repair level of nfi mutant was much lower than its isogenic wild type. However, the pol I proofreading exonuclease deficiency strain KA796 D424A (polA exo-) showed as high repair level as in its isogenic KA796 (polA+). It’s suspected a persistent single strand break was generated due to incomplete repair in KA796 D424A (polA exo-); and in subsequent plasmid replication the dI containing strand was lost because of replication fork collapse. Therefore, only continuous template strand survived the replication and was scored by our assay. This hypothesis was confirmed by using substrate containing both T-I and strand discrimination marker C-C mismatch to determine true repair level. We also used the same substrate for in vitro assay with purified proteins. The result demonstrated that the repair efficiency of the test without polymerase I 3’-5’ exonuclease activity decreased dramatically compared to its isogenic wild type. This observation confirmed our hypothesis and provided solid evidence to support Pol I proofreading exonuclease is the major enzyme activity to remove dI lesion in Endo V repair pathway. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T09:17:59Z (GMT). No. of bitstreams: 1 ntu-106-R04424018-1.pdf: 2070497 bytes, checksum: 39cf6d053f962107f78478a1a98951dc (MD5) Previous issue date: 2017 | en |
| dc.description.tableofcontents | 誌謝 I
中文摘要 II Abstract IV 總目次 VI 圖目次 VIII 表目次 IX 縮寫表 X 第一章 研究背景 1 一、核酸的重要性 1 二、核酸基本修復機制 1 三、次黃嘌呤受損核酸的產生 2 四、次黃嘌呤核苷酸於細胞中的修復路徑 3 五、第五型核酸內切酶修復系統 4 六、第一型去氧核醣核酸聚合酶 5 七、第五型核酸內切酶 6 八、研究動機與目的 7 第二章 實驗材料與方法 10 一、菌株 10 二、載體 10 三、酵素 11 四、具有次黃嘌呤異股核酸質體之設計與建構 11 五、勝任細胞製備與DNA轉型作用 12 六、pBS1雙股核酸之製備 12 七、pBS2單股核酸之製備 14 八、具次黃嘌呤核苷酸鹼基之異雙股核酸之製備 15 九、異雙股核酸對測定用限制酵素之敏感度分析 18 十、細菌體中之修復反應與結果分析 19 十一、以純化蛋白質探討試管中之修復反應與結果分析 20 第三章 結果 22 一、含次黃嘌呤異雙股環狀核酸受質之製備 22 二、含次黃嘌呤核苷酸受質之限制酶敏感度分析 23 三、含次黃嘌呤核苷酸受質於細菌體內修復試驗 24 四、含次黃嘌呤核苷酸受質於純化蛋白質系統之修復試驗 26 第四章 討論 28 一、次黃嘌呤異雙股核酸之設計與建構 28 二、使用phagemid的優點 29 三、T-I核酸受質於細菌體內之修復試驗 30 四、T-I核酸受質於純化蛋白質系統之修復試驗 32 第五章 參考文獻 47 附錄 52 | |
| dc.language.iso | zh-TW | |
| dc.subject | 次黃嘌呤核?酸 | zh_TW |
| dc.subject | 第五型核酸內切? | zh_TW |
| dc.subject | 試管中修復試驗 | zh_TW |
| dc.subject | 第五型核酸內切?修復系統 | zh_TW |
| dc.subject | 細菌體內修復試驗 | zh_TW |
| dc.subject | 第一型核酸聚合? | zh_TW |
| dc.subject | Deoxyinosine | en |
| dc.subject | in vivo repair assay | en |
| dc.subject | in vitro repair assay | en |
| dc.subject | Endo V repair pathway | en |
| dc.subject | DNA polymerase I | en |
| dc.subject | Endonuclease V | en |
| dc.title | 建構含次黃嘌呤之噬菌粒受質以進行試管中及體內第五型核酸內切酶修復分析 | zh_TW |
| dc.title | Construction of phagemid-based deoxyinosine substrate for both in vitro and in vivo endonuclease V repair assay | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 105-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 楊雅倩,蘇剛毅,許濤,蔡芷季 | |
| dc.subject.keyword | 次黃嘌呤核?酸,第五型核酸內切?,第一型核酸聚合?,第五型核酸內切?修復系統,試管中修復試驗,細菌體內修復試驗, | zh_TW |
| dc.subject.keyword | Deoxyinosine,Endonuclease V,DNA polymerase I,Endo V repair pathway,in vitro repair assay,in vivo repair assay, | en |
| dc.relation.page | 60 | |
| dc.identifier.doi | 10.6342/NTU201701401 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2017-07-11 | |
| dc.contributor.author-college | 醫學院 | zh_TW |
| dc.contributor.author-dept | 醫學檢驗暨生物技術學研究所 | zh_TW |
| Appears in Collections: | 醫學檢驗暨生物技術學系 | |
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