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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 李弘文 | |
dc.contributor.author | Yu-Tsung Lee | en |
dc.contributor.author | 李宥宗 | zh_TW |
dc.date.accessioned | 2021-06-08T04:36:03Z | - |
dc.date.copyright | 2011-08-22 | |
dc.date.issued | 2011 | |
dc.date.submitted | 2011-08-17 | |
dc.identifier.citation | 1.Cox, M. M., Recombinational DNA repair of damaged replication forks in Escherichia coli: Questions. Annual Review of Genetics 2001, 35, 53-82.
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J.; Margulie.Ad, Isolation and characterization of recombination-deficient mutants of Escherichia coli K12. Proceedings of the National Academy of Sciences of the United States of America 1965, 53, (2), 451-&. 13.Story, R. M.; Steitz, T. A., Structure of the RecA protein-ADP complex. Nature, 1992, 355, (6358), 374-376. 14.Story, R. M.; Weber, I. T.; Steitz, T. A., The structure of the Escherichia-coli RecA protein monomer and polymer. Nature, 1992, 355, (6358), 318-325. 15.Egelman, E. H., What do X-ray crystallographic and electron-microscopic structural studies of the RecA protein tell us about recombination. Current Opinion in Structural Biology 1993, 3, (2), 189-197. 16.Egelman, E. H.; Stasiak, A., Electron-microscopy of RecA-DNA complexes - two different states, their functional significance and relation to the solved crystal structure. 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M., RecA protein: Structure, function, and role in recombinational DNA repair. In Progress in Nucleic Acid Research and Molecular Biology, Vol. 56, Academic Press Inc: San Diego, 1997; Vol. 56, pp 129-223. 22.Lusetti, S. L.; Cox, M. M., The bacterial REcA protein and the recombinational DNA repair of stalled replication forks. Annual Review of Biochemistry 2002, 71,71-100. 23.Smith, K. C.; Sharma, R. C., A model for the RecA-dependent repair of excision gaps in UV-irradiated Escherichia-coli. Mutation Research 1987, 183, (1), 1-9. 24.Cox, M. M., Motoring along with the bacterial RecA protein. Nature Reviews Molecular Cell Biology 2007, 8, (2), 127-138. 25.Lindsley, J. E.; Cox, M. M., Assembly and disassembly of RecA protein filaments occur at opposite filament ends. Journal of Biological Chemistry 1990, 265, (16), 9043-9054. 26.Shan, Q.; Bork, J. M.; Webb, B. L.; Inman, R. B.; Cox, M. M., RecA protein filaments: End-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins. Journal of Molecular Biology 1997, 265, (5), 519-540. 27.Masui, R.; Mikawa, T.; Kato, R.; Kuramitsu, S., Characterization of the oligomeric states of RecA protein: Monomeric RecA protein can form a nucleoprotein filament. Biochemistry 1998, 37, (42), 14788-14797. 28.Heuser, J.; Griffith, J., Visualization of RecA protein and complexes with DNA by quick-freeze/deep-etch electron microscopy. Journal of Molecular Biology 1989, 210, (3), 473-484. 29.Dicapua, E.; Engel, A.; Stasiak, A.; Koller, T., Characterization of complexes between RecA protein and duplex DNA by electron microscopy. Journal of Molecular Biology 1982, 157, (1), 87-103. 30.Egelman, E. H.; Stasiak, A., Structure of helical RecA-DNA complexes-complexes formed in the presence of ATP-Gamma-S or ATP. Journal of Molecular Biology 1986, 191, (4), 677-697. 31.Norden, B.; Elvingson, C.; Kubista, M.; Sjoberg, B.; Ryberg, H.; Ryberg, M.; Mortensen, K.; Takahashi, M., Structure of RecA DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. Journal of Molecular Biology 1992, 226, (4), 1175-1191. 32.Yu, X.; Egelman, E. H., Structural data suggest that the active and inactive forms of the RecA filament are not simply interconvertible. Journal of Molecular Biology 1992, 227, (1), 334-346. 33.Pugh, B. F.; Schutte, B. C.; Cox, M. M., Extent of duplex DNA underwinding induced by RecA protein-binding in the presence of ATP. Journal of Molecular Biology 1989, 205, (3), 487-492. 34.Madiraju, M.; Lavery, P. E.; Kowalczykowski, S. C.; Clark, A. J., Enzymatic properties of the RecA803 protein, a partial suppressor of RecF mutations. Biochemistry 1992, 31, (43), 10529-10535. 35.Umezu, K.; Kolodner, R. D., Protein interactions in genetic recombination in Escherichia-coli. Journal of Biological Chemistry 1994, 269, (47), 30005-30013. 36.Anderson, D. G.; Kowalczykowski, S. C., The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi- regulated manner. Cell 1997, 90, (1), 77-86. 37.Churchill, J. J.; Anderson, D. G.; Kowalczykowski, S. C., The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of chi, resulting in constitutive recombination activation. Genes & Development 1999, 13, (7), 901-911. 38.Kowalczykowski, S. C.; Clow, J.; Krupp, R. A., Properties of the duplex DNA-dependent ATPase activity of Escherichia-coli RecA protein and its role in branch migration. Proceedings of the National Academy of Sciences of the United States of America 1987, 84, (10), 3127-3131. 39.Pugh, B. F.; Cox, M. M., General mechanism for RecA protein binding to duplex DNA. Journal of Molecular Biology 1988, 203, (2), 479-493. 40.Pugh, B. F.; Cox, M. M., Stable binding of RecA protein to duplex DNA. Journal of Biological Chemistry 1987, 262, (3), 1326-1336. 41.Neuendorf, S. K.; Cox, M. M., Exchange of RecA Protein between adjacent RecA protein-single-stranded DNA complexes. Journal of Biological Chemistry 1986, 261, (18), 8276-8282. 42.Shan, Q.; Cox, M. M., RecA protein dynamics in the interior of RecA nucleoprotein filaments. Journal of Molecular Biology 1996, 257, (4), 756-774. 43.Kubista, M.; Simonson, T.; Sjoback, R.; Widlund, H.; Johansson, A., Towards an understanding of the mechanism of DNA strand exchange mediated by RecA protein. In Biological structure and dynamics, Vols. 1 and 2, Adenine Press {a}: 1996; pp 49-59. 44.Kurumizaka, H.; Rao, B. J.; Ogawa, T.; Radding, C. M.; Shibata, T., A CHIMERIC REC-A PROTEIN THAT IMPLICATES NON-WATSON-CRICK INTERACTIONS IN HOMOLOGOUS PAIRING. Nucleic Acids Research 1994, 22, (16), 3387-3391. 45.Kurumizaka, H.; Shibata, T., Homologous recognition by RecA protein using non-equivalent three DNA-strand-binding sites. Journal of Biochemistry 1996, 119, (2), 216-223. 46.Takahashi, M.; Kubista, M.; Norden, B., Coordination of multiple DNA molecules in RecA fiber evidenced by linear dichroism spectroscopy. Biochimie 1991, 73, (2-3), 219-226. 47.Takahashi, M.; Norden, B., Structure of RecA-DNA complex and mechanism of DNA strand exchange-reaction in homologous recombination. In Advances in Biophysics, Vol 30, 1994, Japan Scientific Soc Press: Tokyo, 1994; Vol. 30, pp 1-35. 48.Pugh, B. F.; Cox, M. M., High salt activation of RecA protein ATPase in the absence of DNA. Journal of Biological Chemistry 1988, 263, (1), 76-83. 49.Shivashankar, G. V.; Feingold, M.; Krichevsky, O.; Libchaber, A., RecA polymerization on double-stranded DNA by using single-molecule manipulation: The role of ATP hydrolysis. Proceedings of the National Academy of Sciences of the United States of America 1999, 96, (14), 7916-7921. 50.Hilario, J.; Amitani, I.; Baskin, R. J.; Kowalczykowski, S. C., Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, (2), 361-368. 51.Ellouze, C.; Selmane, T.; Kim, H. K.; Tuite, E.; Norden, B.; Mortensen, K.; Takahashi, M., Difference between active and inactive nucleotide cofactors in the effect on the DNA binding and the helical structure of RecA filament - Dissociation of RecA-DNA complex by inactive nucleotides. European Journal of Biochemistry 1999, 262, (1), 88-94. 52.Arenson, T. A.; Tsodikov, O. V.; Cox, M. M., Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA. Journal of Molecular Biology 1999, 288, (3), 391-401. 53.Willets, K. A.; Van Duyne, R. P., Localized surface plasmon resonance spectroscopy and sensing. Annual Review of Physical Chemistry 2007, 58, 267- 297. 54.Nie, S. M.; Emery, S. R., Probing single molecules and single nanoparticles by surface-enhanced Raman scattering. Science 1997, 275, (5303), 1102-1106. 55.Schultz, S.; Smith, D. R.; Mock, J. J.; Schultz, D. A., Single-target molecule detection with nonbleaching multicolor optical immunolabels. Proceedings of the National Academy of Sciences of the United States of America 2000, 97, (3), 996-1001. 56.Aslan, K.; Gryczynski, I.; Malicka, J.; Matveeva, E.; Lakowicz, J. R.; Geddes, C. D., Metal-enhanced fluorescence: an emerging tool in biotechnology. Current Opinion in Biotechnology 2005, 16, (1), 55-62. 57.Link, S.; El-Sayed, M. A., Spectral properties and relaxation dynamics of surface plasmon electronic oscillations in gold and silver nanodots and nanorods. Journal of Physical Chemistry B 1999, 103, (40), 8410-8426. 58.Jain, P. K.; Lee, K. S.; El-Sayed, I. H.; El-Sayed, M. A., Calculated absorption and scattering properties of gold nanoparticles of different size, shape, and composition: Applications in biological imaging and biomedicine. Journal of Physical Chemistry B 2006, 110, (14), 7238-7248. 59.Hellen, E. H.; Axelrod, D., Fluorescence emission at dielectric and metal-film interfaces. Journal of the Optical Society of America B-Optical Physics 1987, 4, (3), 337-350. 60.Bohren, C. F.; Huffman, D. R. Absorption and Scattering of Light by Small Particles; Wiley Intersciene: New York, 1983. 61.Xiao, L. H.; Qiao, Y. X.; He, Y.; Yeung, E. S., Three Dimensional Orientational Imaging of Nanoparticles with Darkfield Microscopy. Analytical Chemistry 82, (12), 5268-5274. 62.Xiao, L. H.; Qiao, Y. X.; He, Y.; Yeung, E. S., Imaging Translational and Rotational Diffusion of Single Anisotropic Nanoparticles with Planar Illumination Microscopy. J. Am. Chem. Soc., 2011, 133 (27), 10638–10645 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/22976 | - |
dc.description.abstract | 在生物體內,同源重組反應 (homologous recombination) 是一個關鍵的生化反應,當DNA在複製過程中發生斷裂時進行修補,以維持基因的完整性。在真核生物體進行減數分裂時,同源重組反應的發生,主要是維持基因的異質性。原核生物中的RecA重組酵素和真核生物內有相似功能的蛋白,會和DNA形成核絲蛋白結構,並且尋找互補序列的DNA分子催化和起始同源重組反應。但是RecA和DNA交互作用形成核絲蛋白的機制尚未被完全了解。因此,我們設計了幾個單分子實驗去觀察當RecA酵素在DNA上形成核蛋白絲時,所造成雙股DNA螺旋結構部份解旋的現象。在目前的文獻中,研究團隊大都在DNA的末端接上標誌以放大解旋的過程。本論文主要透過金奈米棒接上DNA的末端,利用暗場顯微技術照射,並且在收光位置裝設在空間上互相正交的二片偏振片,觀察金奈米棒在x軸和y軸上的投影強度變化。藉由投影在二軸上的強度比例,可以獲得金奈米棒在空間上和x軸的夾角。此外,我也在DNA的末端接上一組雙球標誌,此組雙球標誌是由直徑為1微米的磁球和直徑為40奈米的量子點所組成,因磁球散射光和量子點放光在波長上的差異,利用dualview系統分開此二種放光,在攝影機上同時紀錄磁球和量子點的軌跡。此外,當RecA蛋白在雙股DNA上形成核蛋白絲時,DNA會部份解開雙股螺旋結構。架設磁鑷子抑制雙球標誌在溶液中的布朗運動,降低紀錄量子點軌跡時,來自於布朗運動的干擾。同時得到此組雙球的軌跡,進而得到形成核蛋白絲時所造成的螺旋結構解旋資訊。 | zh_TW |
dc.description.abstract | Homologous recombination is a key biochemical process, in which repairing damaged DNA and subsequently maintaining genome integrity takes place among organisms. The recombinase, RecA, in prokaryote plays an important role in initiating and catalyzing the recombination reaction during DNA replication and repairing. It is of great interest to unveil the interaction between RecA and DNA as RecA forming nucleoprotein filament on DNA. To understand how this proceeds, we developed a few single-molecule experiments to detect the rotation of the nucleoprotein filament during the RecA assembly process. In general, this rotation process can be visualized by attaching an object to amplify its rotation process dictated by helical property of the DNA. Here, we demonstrated a single gold nanorod (GNR) method, along with dark field illumination microscopy. By analyzing alternative variations of polarization intensity in x and y directions scattering from gold nanorod coupled to DNA, we can hence resolve angular information during RecA polymerization in real time. We also developed a bead dimer experiment in which one of the end of a single DNA molecule was attached a dimer bead complex composed of a magnetic fluorescent bead and quantum dots with a broad absorption band and narrower fluorescence emission. This method allows us to track the motion of two beads simultaneously during the RecA assembly process. | en |
dc.description.provenance | Made available in DSpace on 2021-06-08T04:36:03Z (GMT). No. of bitstreams: 1 ntu-100-R98223117-1.pdf: 1920699 bytes, checksum: a69b9b01079d7b51db67a7841c7a4dca (MD5) Previous issue date: 2011 | en |
dc.description.tableofcontents | 章節目錄
第一章緒論 1 1-1 同源重組 (Homologous Recombination) 1 1-2 RecA重組酵素 4 1-3 RecA 蛋白與DNA 的交互作用 8 1-4 RecA 蛋白水解三磷酸腺苷 11 第二章實驗原理 12 2-1 金奈米粒子表面電漿共振效應 12 2-2 金奈米粒子表面電子振動之電磁理論 13 2-3 金奈米棒三維位向資訊解析 16 第三章實驗設計 19 3-1 金奈米棒暗場影像實驗 19 3-1-1 DNA 製備 19 3-1-2 玻片之表面修飾 20 3-1-2-1 Flow Chamber 製備 20 3-1-2-2 玻片表面修飾 21 3-1-3 暗場顯微技術 (Darkfield Microscopy) 23 3-1-4 偵測散射光 24 3-1-5 數據分析 25 3-2 雙球標誌觀測在 RecA 蛋白催化下雙股去氧核醣核酸部份解旋過程 27 3-2-1 DNA 製備 27 3-2-2 玻片之表面修飾 28 3-2-3 製備表面修飾 streptavidin 的磁球 29 3-2-4 製備表面修飾 biotin 的 polystyrene 圓球 30 3-2-5 螢光顯微鏡 31 第四章實驗結果 33 4-1 金奈米棒暗場影像實驗 33 4-1-1 具備偵測金奈米棒旋轉的靈敏度 33 4-1-2 金奈米棒在雙股 DNA 轉動布朗運動 37 4-1-3 RecA 蛋白嵌入 DNA 後,金奈米棒的旋轉布朗運動 39 4-2 雙球標誌觀測在 RecA 蛋白催化下雙股去氧核醣核酸部份解旋過程 40 4-2-1 DIC 影像觀測 DNA 雙股螺旋的部份解旋過程 40 4-2-2 螢光影像觀測 DNA 雙股螺旋的部份解旋過程 42 第五章總結與未來展望 44 參考文獻 45 | |
dc.language.iso | zh-TW | |
dc.title | 直接觀察RecA重組酶形成核蛋白絲時雙股去氧核醣核酸螺旋結構的旋轉過程 | zh_TW |
dc.title | Direct observation of DNA rotation during RecA nucleoprotein filament formation | en |
dc.type | Thesis | |
dc.date.schoolyear | 99-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 張煥宗,陳俊顯,范秀芳 | |
dc.subject.keyword | RecA重組酶,核蛋白絲,金奈米棒,暗場顯微鏡, | zh_TW |
dc.subject.keyword | RecA,nucleoprotein filament,gold nanorod,darkfield microscopy, | en |
dc.relation.page | 51 | |
dc.rights.note | 未授權 | |
dc.date.accepted | 2011-08-17 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 化學研究所 | zh_TW |
顯示於系所單位: | 化學系 |
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