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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/47739完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 李弘文 | |
| dc.contributor.author | Mu-Ni Hsu | en |
| dc.contributor.author | 徐慕霓 | zh_TW |
| dc.date.accessioned | 2021-06-15T06:15:44Z | - |
| dc.date.available | 2012-08-16 | |
| dc.date.copyright | 2010-08-16 | |
| dc.date.issued | 2010 | |
| dc.date.submitted | 2010-08-11 | |
| dc.identifier.citation | 1 Nelson, D. L., Cox, M. M. (2008) Lehninger principles of biochemistry, 5th ed., W. H. Freeman, New York.
2 Cox, M. M., (2003) The bacterial RecA protein as a motor protein. Annu. Rev. Microbiol. 57, 551-577 3 Kowalczykowski, S. C., Eggleston, A. K., (1994)Homologous pairing and DNA strand exchange protein. Annu. Rev. Biochem. 63, 991-1043 4 Cox, M.M. (2007) The bacterial RecA protein: structure, function, and regulation. In Topics in Current Genetics. Molecular Genetics of Recombination. (A. Aguilera and R. Rothstein, eds.) (Springer-Verlag GmbH, Heidelberg, Germany). Vol. 1, pp.53-94. 5 Smith, G. R. (1983) General recombination, p. 175-209. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, R. A. Weisberg (ed.), LambdaII. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 6 Clark, A. J., and A. D. Margulies. (1965) Isolation and characterization of recombination-deficient mutants of E. coli K-12. Proc.Natl. Acad. Sci. U. S. A. 3, 451-459. 7 Smith, K. C., and R. C. Sharma. (1987) A model for the recA-dependent repair of excision gaps in UV-irradiated Escherichia coli. Mutat. Res. 183, 1-9. 8 Lusetti, S.L., and Cox, M.M. (2002) The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu. Rev. Biochem. 71, 71-100 9 Story, R. M., Weber, I. T. and Steitz, T. A. (1992) The structure of the E. coli recA protein monomer and polymer. Nature 355, 318-325 10 Cox, M. M., (2007) Motoring alone with the bacterial RecA protein. Nature Rev. Mol.Cell Biol. 8, 127-138 11 Konola, J. T., Logan, K. M., Knight, K. L., (1994) Functional Characterization Residues in the P-loop Motif of the RecA Protein ATP Binding Site. J. Mol. Biol. 237, 20-34 12 Rehrauer, W. M., Kowalczykowski, S. C. (1993) Alteration of he nucleoside triphosphate (NTP) catalytic domain within Escherichia coli recA protein attenuates NTP hydrolysis but not joint molecule formation. J. Biol. Chem. 268, 1292-1297 13 Kwumizaka, H., Rao, B.J., Ogawa, T., Radding, C. M., Shibata, T., (1994) A chimeric Rec-A protein that implicates non-Watson-Crick interactions in homologous pairing. Nucleic Acids Res. 22, 3387-3391 14 Cox, M. M. (1995) Alignment of 3 (but not 4) DNA trands within a RecA protein filament. J. Biol. Chem. 270, 26021-26024. 15 Heuser, J., Griffith, J. (1989) Visualization of RecA protein and its complexes with DNA by quick-freeze/deep-etch electron microscopy. J. Mol. Biol. 210, 473-484 16 Nordh, B., Elvingson, C., Kubista, N., Sjoberg, B., Ryberg, H., Ryberg, M., Mortensen, K., Takahashi, M. (1992) Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J. Mol. Biol. 226, 1175-1191 17 Pugh, B. F., Cox, M. M. (1987) Stable binding of RecA protein to duplex DNA. unraveling a paradox. J. Biol. Chem. 262, 1326-1336 18 Pugh, B. F., Schutte, B. C., Cox, M. M. (1989) Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP. J. Mol. Biol. 205, 487-492 19 McEntee K., Weinstock G. M., Lehman I.R. (1980) recA protein-catalyzed strand assimilation: stimulation by Escherichia coli single-stranded DNA-binding protein. Proc. Natl. Acad. Sci. U. S. A. 77, 857-861 20 Cox, M. M., Soltis, D. A., Livneh, Z. and Lehman, I. R. (1983). On the role of single-stranded DNA binding protein in recA protein-promoted DNA strand exchange. J. Biol. Chem. 258, 2577-2585. 21 Kowalczykowski, S. C., Krnpp, R.A. (1987) Effect of Escherichia coli SSB protein on the single-stranded DNA-dependent ATPase activity of Escherichia coli RecA protein: Evidence that SSB protein facilitates the binding of RecA protein to regions of secondary structure within single stranded DNA. J. Mol. Biol. 193, 97-113 22 Register III, J. C., Griffith, J. (1985) The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange. J. Biol. Chem. 260, 12308-12312 23 Dutreix, M., Rao, B. J., Radding, C. M. (1991) The effects on strand exchange of 5’ versus 3’ ends of single-stranded DNA in RecA nucleoprotein filaments. J. Mol. Biol. 219,645-654 24 Lindsley, J. E., Cox, M. M. (1990). Assembly and disassembly of recA protein filaments occur at opposite filament ends. Relationship to DNA strand exchange. J. 55 Biol. Chem. 265, 9043-9054. 25 Ellouze C, Selmane T, Kim HK, Tuite E, Norden B, Mortensen K, Takahashi M (1999) 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. Eur. J. Biochem. 262, 88-94 26 Arenson TA, Tsodikov OV, Cox MM (1999) Quantitative analysis of the kinetics of end-dependent disassembly of RecA filament from ssDNA. J. Mol. Biol. 288, 391-401 27 Shan, Q., Bork, J. M., Webb, B. L., Inman, R. B., Cox, M. M. (1997) RecA protein filaments: End-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins. J. Mol. Biol. 265, 519–40 28 Weinstock, G. M., McEntee K., Lehman, I.R. (1981) Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Characterization of ATP hydrolysis. J. Biol. Chem. 256, 8829-8834 29 Yu X, Egelman EH (1992) Stucture data suggest that the active and inactive forms of the RecA filament are not simply interconvertible. J. Mol. Biol. 227, 334-346 30 Lusetti, S., Shaw, J. and Cox, M.M. (2003) Magnesium ion-dependent activation of the RecA protein involves the C terminus. J. Biol. Chem. 278, 16381-16388. 31 Haruta, N., Yu, Xiong, Yang, Shixin, Egelman, Edward H., and Cox, M.M. (2003) A DNA pairing-enhanced conformation of bacterial RecA proteins. J. Biol. Chem. 278, 52710-52723. 32 Kowalczykowski, S.C. and Eggleston, A.K. (1994). Homologous pairing and DNA strand exchange proteins. Annu. Rev. Biochem. 63, 991-1043. 33 Roca, A. L. and Cox, M. M. (1997). RecA protein: Structure, function, and role in recombinational DNA repair. In Progress in Nucleic Acid Research and Molecular Biology. W. E. Cohn and K. Moldave, eds. (Academic Press, Inc., San Diego, CA), Vol. 56, pp. 129-223. 34 Kowalczykowski, S.C. and Krupp, R.A. (1995). DNA strand exchange promoted by RecA protein in the absence of ATP: Implications for the mechanism of energy transduction in protein-promoted nucleic acid transactions. Proc. Natl. Acad. Sci. U. S. A. 92, 3478-3482. 35 Shan, Q., Cox, M. M. and Inman, R. B. (1996). DNA strand exchange promoted by RecA K72R: Two reaction phases with different Mg2+ requirements. J. Biol. Chem. 56 271, 5712-5724. 36 Jain, S. K., Cox, M. M. and Inman, R. B. (1994). On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. III. Unidirectional branch migration and extensive hybrid DNA formation. J. Biol. Chem. 269, 20653-20661. 37 West SC, Cassuto E, Howard-Flanders P (1981) Heteroduplex formation by RecA protein: polarity of strand exchanges. Proc. Natl. Acad. Sci. U. S. A. 78, 6149-6153 38 Bedale, W. A. and Cox, M. M. (1996). Evidence for the coupling of ATP hydrolysis to the final (extension) phase of RecA protein-mediated DNA strand exchange. J. Biol. Chem. 271, 5725-5732. 39 Kim, J.-I., Cox, M. M. and Inman, R. B. (1992). On the role of ATP hydrolysis in recA protein-mediated DNA strand exchange: I. Bypassing a short heterologous insert in one DNA substrate. J. Biol. Chem. 267, 16438-16443. 40 Kim, J.-I., Cox, M. M. and Inman, R. B. (1992). On the role of ATP hydrolysis in recA protein-mediated DNA strand exchange: II. Four-strand exchanges. J. Biol. Chem. 267,16444-16449. 41 Howard-Flanders P, West SC, Stasiak A (1984) Role of RecA protein spiral filament in genetic recombination. Nature 309,215-219 42 Müller B, Koller T, Stasiak A (1990) Characteriztion of the DNA binding activity of stable RecA-DNA complexes: interaction between the two DNA binding sites within RecA helical filament. J. Mol. Biol. 212, 97-112 43 Chow SA, Chiu SK, Wong BC (1992) RecA protein-prommmoted homologous pairing and strand exchange between intact and partially single-stranded duplex DNA. J. Mol. Biol. 223,79-93 44 Shan, Q. and Cox, M.M. (1998). On the mechanism of RecA-mediated repair of double strand breaks: No role for four-strand DNA pairing intermediates. Mol. Cell 1, 309-317. 45 Xiao, J., Singleton, S.F. (2002) Elucidating a key intermediate in homologous DNA strand exchange: Structural characterization of the RecA-triple-stranded DNA complex using fluorescence resonance energy transfer. J. Mol. Biol. 320, 529-558 46 Gupta, R. C., Folta-Stogniew, E., O’Malley, S., Takahashi, M., Radding, C. M. (1999) Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein. Mol. Cell 4,705-714 47 Adzuma, K. (1992) Stable synapsis of homologous DNA molecules mediated by the 57 Escherichia coli RecA protein involves local exchange of DNA strands. Genes Dev. 6, 1679-1694 48 Bazemore L. R., Takahashi M., Radding C. M. (1997) Kinetic analysis of pairing and strand exchange catalyzed by RecA. Detection by fluorescence energy transfer. J. Biol. Chem. 272, 14672-14682 49 Folta-Stogniew, E., O’Malley, S., Gupta, R., Anderson, K. S., Radding, C. M. (2004) Exchange of DNA base pairs that coincides with recognition of homology promoted by E. coli. RecA protein. Mol. Cell 15, 965-975 50 Konforti, B. B., Davis, R. W. (1992) ATP hydrolysis and the displaced strand are two factors that determine the polarity of RecA-promoted DNA strand exchange. J. Mol. Biol. 227, 38-53 51 Cox, M. M. (1994) Why does RecA protein hydrolyze ATP? Trends Biochem. Sciences 19, 217-222. 52 Jwang, B., Radding, C. M. (1992) Torsional stress generated by RecA protein during DNA strand exchange separates strands of heterologous insert. Proc. Natl. Acad. Sci. U. S. A. 89,7596-7600 53 MacFarland, K. J., Shan, Q., Inman, R. B. and Cox, M. M. (1997). RecA as a motor protein: testing models for the role of ATP hydrolysis in DNA strand exchange. J. Biol. Chem. 272, 17675-17685. 54 Bockelmann, U. (2004) Single-molecule manipulation of nucleic acids. Curr. Opin. Struct. Biol. 14, 368-373 55 Gosse, C., Croquette, V. (2002) Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys. J. 82, 3314-3329 56 Yin, H., Landick, R. and Gelles J. (1994) Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys. J. 67, 2468-2478 57 Schafer, D. A., Gelles. J., Sheez, M. P. and Landick R. (1991) Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352, 444-448 58 Han, L., Garcia, H. G., Blumberg, S., Towles, K. B., Beausang, J. F., Nelson, P. C., Philips, R. (2009) Concentration and length dependence of DNA looping in transcriptional regulation. PLoS One 4, e5621 59 Fan H-F, Cox MM, & Li H-W (2010) Using real-time, single-molecule experiments to monitor RecA-mediated paring and strand exchange reaction in various nucleotide 58 states Manuscript (in eng). 60 Conley, E. C., West, S. C. (1990) Underwinding of DNA associated with duplex-duplex pairing by RecA protein. J. Biol. Chem. 265, 10156-10163 61 Ali, J. A. and Lohman, T. M. (1997) Kinetic measurement of the step size of DNA ubwinding by Escherichia coli UvrD helicas. Science 275, 377-380 62 Cassuto, E., West, S. C., Mursalim, J., Conlon, S., Howard-Flanders, P. (1980) Initiation of genetic recombination: homologous pairing between duplex DNA molecules promoted by recA protein. Proc. Natl. Acad. Sci. U. S. A. 77, 3962-3966 63 Yancey-Wrona, J. E. and Camerini-Otero, R. D. (1995) The search for DNA homology does not limit stable homologous pairing promoted by RecA protein. Curr. Biol. 5, 1149-1158 64 Ullsperger, C. J., Cox, M. M. (1995) Quantitative RecA protein binding to the hybrid duplex product of DNA strand exchange. Biochem. 34, 10859-10866 65 Julin, D. A., Riddling, C. M. (1986) On the mechanism of pairing of single- and double- stranded DNA molecules by recA and single-stranded DNA-binding proteins | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/47739 | - |
| dc.description.abstract | 大腸桿菌在複製DNA 的過程中，因為DNA 的斷裂而造成複製過程中止，產生double-strand break，修補的途徑為同源重組反應，其中的核心步驟在於RecA 與DNA 形成的核絲結構可辨認相同序列的DNA 分子，並催化交換反應的進行。雖然細菌體的RecA 較廣泛的被研究，但真核生物體中皆已發現相似功能的蛋白存在，且交換反應的步驟大致可分為RecA 先與其中一條具有單股結構的DNA 鍵結，催化兩條相同序列的DNA 分子交換，RecA 隨後與DNA 分子脫離。同源重組反應中所牽涉到的交換反應是四股系統，以往的研究多著重於三股交換系統，且無法有效區別交換反應中各步驟的作用。論文中以單分子TPM 實驗直接觀察RecA所催化的四股交換反應，藉固定於玻片上的DNA 分子因四股交換反應發生而離去的比例，獲得四股交換反應的性質。首先，分別在ATP 及ATPγS 的條件下反應，ATPγS 是與ATP 結構相近卻無法被RecA 水解的分子，發現四股交換反應需要水解ATP。再以不同位置的單股缺口DNA 進行實驗，在我們所設計的DNA 長度下，四股交換反應沒有偏好特定位置的單股結構。並嘗試建立“n-step”動力學模型描述四股交換的反應機制，提出交換反應的進行是以相同的速率重複交換一定長度的DNA 分子。擬合結果顯示四股交換反應的速率常數與過去三股交換反應研究的速率常數值接近，當參與交換反應的DNA 分子，單股突出長度近百個鹼基對且為5'端overhang 時，四股交換反應速率大於單股突出長度較短或是3'端overhang 的其他組實驗。 | zh_TW |
| dc.description.abstract | E. coli RecA protein is required for repairing damaged DNA through homologous recombination pathway. The assembled RecA/DNA nucleoprotein filaments catalyze the reactions that paired and exchange with homologous DNA sequence. We used single-molecule tethered particle motion (TPM) experiments to directly observe the strand exchange process catalyzed by RecA in real-time. The surface-bound DNA is a duplex DNA with a bead could be displaced due to four-strand exchange. Calculate the percentage of leaving tethers under different condition to obtain the properties of four-strand exchange. The RecA-mediated strand exchange efficiency is higher for ATP than ATPγS, suggesting that ATP hydrolysis by RecA is required to complete strand
exchange. In addition, the RecA-mediate strand exchange is shown to progress either from 5’end or from 3’end in our experiment. Furthermore quantitative analysis of DNA exchanging time courses using ‘‘n-step’’ sequential mechanisms, can reveal information about the rate constant of four-strand exchange reaction and the average number of basepairs in the strand exchange cycle. The result indicates that the rate is larger for longer single-stranded gap and 5’overhang. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T06:15:44Z (GMT). No. of bitstreams: 1 ntu-99-R97223109-1.pdf: 3775942 bytes, checksum: 46c05c5869c50e6ebbf70c2d77c14ab6 (MD5) Previous issue date: 2010 | en |
| dc.description.tableofcontents | 第一章緒論 1
1-1 同源重組(Homologous recombination) 1 1-2 RecA 蛋白及其結構 3 1-3 RecA 蛋白與DNA 的作用 6 1-3.1 與DNA 鍵結(binding) 6 1-3.2 RecA 絲狀結構的形成 7 1-3.3 RecA 水解三磷酸腺苷 8 1-4 RecA 蛋白調控的DNA 交換反應(strand exchange) 10 1-4.1 DNA 的配對(pairing) 12 1-4.2 交換反應的機制 14 1-5 Tethered Particle Motion (TPM) 17 1-6 研究動機 18 第二章 實驗架構 19 2-1 DNA 的製備 19 2-2 Flow Chamber 的製備 22 2-3 製備表面修飾Streptavidin 的球 23 2-4 四股交換反應(four-stranded exchange reaction) 25 2-4.1 單分子實驗 25 2-4.2 Bulk 實驗 26 2-5 影像擷取和數據分析 26 第三章 實驗結果與討論 27 3-1 ATP 水解對四股交換反應的影響 27 3-1.1 實驗設計 27 3-1.2 四股交換反應需要水解ATP 28 3-2 不同位置的單股突出(overhang)DNA 對四股交換反應的影響 30 3-2.1 不同位置的單股突出DNA 四股交換完成的比例 30 3-2.2 不同位置的單股突出DNA 四股交換起始的比例 33 3-2.2 離去DNA 布朗運動隨時間的變化 35 3-3 “n-step” kinetic mechanism 37 第四章 總結與未來展望 45 4-1 論文總結 45 4-2 未來展望 45 附錄 46 A. 以拉普拉斯轉換(Laplace transform)的方法解“n-step” mechanism 46 B. Invasion Strand Experiments 49 C. 其他實驗設計探討四股交換反應 51 參考資料 53 | |
| dc.language.iso | zh-TW | |
| dc.subject | DNA修復 | zh_TW |
| dc.subject | 單分子栓球實驗 | zh_TW |
| dc.subject | 同源重組 | zh_TW |
| dc.subject | RecA蛋白 | zh_TW |
| dc.subject | 四股交換 | zh_TW |
| dc.subject | four-strand exchange | en |
| dc.subject | TPM | en |
| dc.subject | homologous recombination | en |
| dc.subject | RecA | en |
| dc.subject | DNA repair | en |
| dc.title | RecA 重組酶的四股交換反應機制 | zh_TW |
| dc.title | Direct Observation of RecA-Mediated Four-strand Exchange
at the Single-Molecule Level | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 98-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 陳長謙,蘇志明,詹迺立,范秀芳 | |
| dc.subject.keyword | RecA蛋白,四股交換,DNA修復,同源重組,單分子栓球實驗, | zh_TW |
| dc.subject.keyword | RecA,four-strand exchange,DNA repair,homologous recombination,TPM, | en |
| dc.relation.page | 58 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2010-08-11 | |
| 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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