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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 李弘文(Hung-Wen Li) | |
| dc.contributor.author | Tzu-Yu Lee | en |
| dc.contributor.author | 李子于 | zh_TW |
| dc.date.accessioned | 2023-03-19T22:12:54Z | - |
| dc.date.copyright | 2022-10-19 | |
| dc.date.issued | 2022 | |
| dc.date.submitted | 2022-09-25 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/84479 | - |
| dc.description.abstract | RAD51同源同種物（paralog）是參與同源重組（homologous recombination）修復的重要蛋白。BCDX2是由RAD51同源同種物RAD51B、RAD51C、RAD51D、及XRCC2組成的蛋白複合體，被認為能協助RAD51聚集。我使用了三種單分子螢光方法了解BCDX2是否影響RAD51和DNA的結合。螢光標記蛋白和零模波導（zero-mode waveguides）的螢光實驗發現BCDX2和DNA的結合反應是一動態過程，且在RAD51存在時結合能力下降。單分子螢光共振能量轉移（FRET）實驗發現，在含有BCDX2的情況下，RAD51蛋白絲對單股和雙股DNA所產生的拉伸效果並未受到影響。然而，BCDX2在有ATP的條件之下提昇了RAD51在雙股DNA上的蛋白誘導之螢光增強效應（protein-induced fluorescence enhancement）。此效應與反應時間相關，且可能反映出ATP水解反應的參與。這些觀察為未來研究BCDX2在同源重組中扮演的角色，提供新的資訊。 | zh_TW |
| dc.description.abstract | RAD51 paralogs are important proteins that participate in homologous recombination repair. One of the heteromeric complexes BCDX2 (RAD51B-RAD51C-RAD51D-XRCC2) is hypothesized to stimulate RAD51 foci formation. I used three single-molecule fluorescence tools to investigate how BCDX2 affects the RAD51 binding. Using fluorescently labeled protein and zero-mode waveguides, BCDX2 binding to DNA was found to be dynamic and reduced by RAD51. Single-molecule fluorescence resonance energy transfer (FRET) showed that BCDX2 does not alter the DNA extension property of RAD51 on single-strand DNA (ssDNA) or double-strand DNA (dsDNA). However, protein-induced fluorescence enhancement (PIFE) results showed that BCDX2 increased the PIFE effect of RAD51 on dsDNA but not ssDNA in the presence of ATP, in a time-dependent manner. This PIFE increase is potentially linked to ATP hydrolysis. These observations provide new information to elucidate the roles of BCDX2 in homologous recombination. | en |
| dc.description.provenance | Made available in DSpace on 2023-03-19T22:12:54Z (GMT). No. of bitstreams: 1 U0001-2309202211530700.pdf: 5587021 bytes, checksum: 70396612228c10d35323d07d79e7552e (MD5) Previous issue date: 2022 | en |
| dc.description.tableofcontents | Contents 謝辭 i 摘要 iii Abstract iv List of Figures vii List of Tables viii 1 Introduction 1 2 Methods and Materials 6 2.1 DNA substrate preparation 6 2.1.1 DNA substrate labeling 6 2.1.2 Annealing 7 2.2 Microscope chamber making 9 2.2.1 Coverslips for TIRF imaging 9 2.2.2 Zero-mode waveguide 10 2.3 Single-molecule imaging and data acquisition 11 2.4 BCDX2-SNAP-647 binding assay 12 2.5 RAD51 filament FRET assay 13 2.6 Protein induced fluorescence enhancement (PIFE) assay 14 2.7 Data analysis 14 2.7.1 Image registration 14 2.7.2 Intensity calculation 16 2.7.3 PIFE calcualtion 17 3 Results 19 3.1 BCDX2 binds to DNA dynamically 19 3.2 BCDX2 did not alter the FRET distribution of RAD51 filament 22 3.3 BCDX2 altered RAD51 binding on dsDNA in the presence of ATP 24 4 Discussions 31 4.1 Future perspective 34 Bibliography 36 A Supplementary figures 46 B List of materials 53 List of Figures 2.1 DNA substrates used in this study 7 3.1 BCDX2-SNAP-647 binding to DNA was monitored using ZMWs. 21 3.2 BCDX2-SNAP-647 binding was reduced by RAD51. 23 3.3 BCDX2 did not cause significant FRET distribution change at three different DNA segments. 24 3.4 BCDX2 did not alter the RAD51-induced PIFE for substrate I. 27 3.5 BCDX2 induced a PIFE increase for substrate II. 29 3.6 The BCDX2-induced PIFE increase on substrate II was time-dependent. 30 A.1 BCDX2 non-specific binding on ZMWs was limited. 47 A.2 Binding of 250 nM BCDX2-SNAP-647. 48 A.3 Naive BCDX2 bound fraction estimates at different RAD51 concentrations. 49 A.4 Probability density estimates for the pooled FRET efficiency data. 49 A.5 ECDF plots of the relative intensity for substrate I. 50 A.6 ECDF plots of the relative intensity for substrate II. 51 A.7 Proposed models. 52 List of Tables 2.1 DNA oligonucleotides used in this study. 8 3.1 Two-sample Anderson-Darling test results for pooled FRET values comparing the absence and presence of BCDX2. 25 | |
| dc.language.iso | en | |
| dc.subject | RAD51 | zh_TW |
| dc.subject | 單分子螢光 | zh_TW |
| dc.subject | BCDX2蛋白複合體 | zh_TW |
| dc.subject | RAD51同源蛋白 | zh_TW |
| dc.subject | 同源重組 | zh_TW |
| dc.subject | RAD51 paralogs | en |
| dc.subject | single-molecule fluorescence | en |
| dc.subject | BCDX2 complex | en |
| dc.subject | RAD51 | en |
| dc.subject | homologous recombination | en |
| dc.title | 利用單分子螢光方法觀察RAD51及其同源蛋白之交互作用 | zh_TW |
| dc.title | Using Single-Molecule Fluorescence Methods to Study the Interaction of RAD51 and Its Paralogs | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 110-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.author-orcid | 0000-0002-9349-2897 | |
| dc.contributor.oralexamcommittee | 冀宏源(Hung-Yuan Chi),章為皓(Wei-Hau Chang) | |
| dc.subject.keyword | 同源重組,RAD51,RAD51同源蛋白,BCDX2蛋白複合體,單分子螢光, | zh_TW |
| dc.subject.keyword | homologous recombination,RAD51,RAD51 paralogs,BCDX2 complex,single-molecule fluorescence, | en |
| dc.relation.page | 55 | |
| dc.identifier.doi | 10.6342/NTU202203886 | |
| dc.rights.note | 同意授權(限校園內公開) | |
| dc.date.accepted | 2022-09-26 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 化學研究所 | zh_TW |
| dc.date.embargo-lift | 2024-09-30 | - |
| 顯示於系所單位： | 化學系 | |
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