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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 溫進德 | |
| dc.contributor.author | Cheng-Han Wu | en |
| dc.contributor.author | 吳承翰 | zh_TW |
| dc.date.accessioned | 2021-06-16T23:15:05Z | - |
| dc.date.available | 2012-08-10 | |
| dc.date.copyright | 2012-08-10 | |
| dc.date.issued | 2012 | |
| dc.date.submitted | 2012-08-01 | |
| dc.identifier.citation | Abels, J. A., F. Moreno-Herrero, et al. (2005). 'Single-molecule measurements of the persistence length of double-stranded RNA.' Biophys J 88(4): 2737-2744.
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/65011 | - |
| dc.description.abstract | 在細胞中，轉譯（translation）的過程是受到高度調控的。我們在此將焦點放在大腸桿菌（Escherichia coli）rpsO基因所轉譯的核醣體蛋白 S15（ecS15）上。核醣體蛋白 S15可以結合到自身的信使核醣核酸（mRNA）上5’端未轉譯區，並且在核醣體蛋白 S15過剩時抑制其轉譯的進行；此結合而抑制的效果發生在信使核醣核酸的這段摺疊成假結（pseudoknot）結構的區域，然而這段區域也可以摺疊成雙髮夾（double-hairpin）的結構。再者，SD序列（Shine-Dalgarno sequence）只會暴露在假結的構形上並允許核醣體結合且解開此構造來起始轉譯。當核醣體蛋白 S15表現過量時，它可以結合至假結的結構導致核醣體被困在前起始階段。
rpsO信使核醣核酸上5’端未轉譯區所形成的結構在過去研究已甚了解，但雙髮夾的形成角色並不知道。為了了解這段5’端未轉譯區結構上和動力學上的特性，我們利用光鉗（optical tweezers）解開此核醣核酸片段。這個技術讓我們可以觀察到單一核醣核酸分子的構形改變（conformational change）。我們發現雙髮夾的形成可以促使其重組成假結結構，儘管假結的摺疊也可以不經由雙髮夾的結構。此外，我們還發現其他的結構產生，他們在光鉗上所表現出來的特性和假結類似。從我們實驗的結果推論雙髮夾結構在摺疊過程中是一種中間物，需要其他因子或蛋白來協助假結的正確構成。 | zh_TW |
| dc.description.abstract | Translation is a highly regulated process in the cell. Here, we have focused on the translational regulation of Escherichia coli ribosomal protein S15 (ecS15), which is encoded by the rpsO gene. The ecS15 can bind to the 5’ untranslated region (5’-UTR) of its own mRNA and repress its translation when the ecS15 is in excess; the binding repression occurs when this region of the mRNA folds into a unique pseudoknot structure, as opposed to an alternative double-hairpin structure. However, the Shine-Dalgarno (SD) sequence is only exposed on the pseudoknot form to allow the ribosome binding and melting this structure for the initiation of translation. When ecS15 is over expressed, it binds to the pseudoknot and leads to the ribosome trapped in the pre-initiation state.
The 5’-UTR of the rpsO mRNA has been studied for alternative structure formation in the past, but the role of the double-hairpin structure is unknown. To characterize these structural and dynamic aspects, we used optical tweezers to unfold the 5’-UTR of the rpsO mRNA. This technique allows us to observe the conformational change of a single RNA molecule. We find that formation of the pseudoknot can be promoted from rearrangement of the double-hairpin structure. In addition, we also observed some other structures of which the full unfolding distance is similar to that of the pseudoknot. From our results, we suggest that the double-hairpin may be an intermediate on the folding pathway to the pseudoknot, and other factors or proteins are required to promote correct formation of the pseudoknot structure. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T23:15:05Z (GMT). No. of bitstreams: 1 ntu-101-R99b43018-1.pdf: 1353305 bytes, checksum: 279f475b0d413a126b8ff3cd0eafcbff (MD5) Previous issue date: 2012 | en |
| dc.description.tableofcontents | Contents
摘要............................................................................................................................i Abstract…………………………………………………………………………….ii Contents…………………………………………………………………………… iii List of Tables……………………………………………………………………… vi List of Figures………………..………………………………………………........ vii Chapter 1 – Introduction………………………………………………………… 1 1.1 Translation…………………………………………………………………… 1 1.1.1 The Ribosome and Ribosomal Protein S15…………………………….. 1 1.1.2 Translational regulation of Ribosomal Protein S15…………………….. 2 1.1.3 Rearrangement of RNA Structures……………………………………... 2 1.2 Single-Molecule Techniques………………………………………………… 3 1.2.1 Applications of Single-Molecule Force Spectroscopy Techniques…….. 3 1.2.2 Measurements of RNA Folding and Unfolding by Optical Tweezers….. 6 Chapter 2 – Materials and Methods……………………………………………. 7 2.1 Materials…………………………………………………………………….. 7 2.1.1 Bacterial Strains………………………………………………………... 7 2.1.2 Plasmid Vectors………………………………………………………… 7 2.1.3 Oligomers and Primers…………………………………………………. 7 2.1.4 Enzymes……………………………………………………………….. 10 2.1.5 Chemicals……………………………………………………………… 11 2.1.6 Kits…………………………………………………………………….. 12 2.1.7 Buffers…………………………………………………………………. 13 2.2 Methods…………………………………………………………………….. 13 2.2.1 Plasmid Construction………………………………………………….. 13 2.2.2 In-vitro Transcription…………………………………………………... 14 2.2.3 PCR for DNA Handles…………………………………………………. 14 2.2.4 5’-Handles Modification………………………………………………. 14 2.2.5 Annealing of Handles to RNA…………………………………………. 15 2.2.6 Pulling Test by Optical Tweezers………………………………………. 15 Chapter 3 – Results……………………………………………………………… 17 3.1 Purification of RNA transcripts and DNA Handles………………………… 17 3.2 S15WT RNA Pseudoknot Is Stabilized by Mg2+ Ions……………………. 17 3.3 Force-Extension Patterns of S15WT in 20 mM Mg2+…………………….. 18 3.3.1 Hairpin Structures Can Be Rearranged to Pseudoknots at Low Forces.. 19 3.4 Further Characterization of the Double-hairpin and Pseudoknot Structures.. 19 3.4.1 S15mPK……………………………………………………………….. 19 3.4.2 S15mHP……………………………………………………………….. 20 3.5 Characterization of the 2T and 2CT Unfolding patterns…………………… 20 3.5.1 S15mP/G………………………………………………………………. 21 3.5.2 S15mH/G………………………………………………………………. 22 3.6 Refolding Measurements of S15WT and the mutants……………………… 22 Chapter 4 – Discussions………………………………………………………… 23 4.1 Mg2+ Ion Effects on Tertiary Structures…………...……………………….. 23 4.2 Formation of the Stem 2 Can Promote Rearrangement for Pseudoknot…… 23 4.3 Tertiary Structure Folding for Other Transition Patterns…………………… 24 4.4 Interaction with the S15 protein……….…………………………………… 26 References………………………………………………………………………… 27 List of Tables Table 1 The characteristics of the unfolding transitions of the S15WT……………...36 Table 2 Average unfolding forces of different patterns for the five RNA constructs in 20 mM MgCl2………………………………………………………………..37 Table 3 Average extension values of different patterns for the five RNA constructs in 20 mM MgCl2………………………………………………………………..38 Table 4 The population of the unfolding transitions for the four RNA constructs in 20 mM MgCl2………………………………………………………………..39 Table 5 The characteristics of the refolding transitions of the S15WT………………40 List of Figures Figure 1 Schematic diagrams for single-molecule optical tweezers experiments…...41 Figure 2 The S15WT RNA construct ………………………………….……………42 Figure 3 The S15mPK and S15mHP mutants……………………………………….43 Figure 4 The S15mP/G and S15mH/G mutants……………………………………..44 Figure 5 Design of DNA handles……………………………………………………45 Figure 6 Purification of all RNAs……………………………………………………46 Figure 7 PCR for DNA handles……………………………………………………...47 Figure 8 Force-extension curves of the S15WT……………………………………..48 Figure 9 Force-extension patterns of S15WT in 20 mM MgCl2….………………....49 Figure 10 Distribution of the first unfolding force for S15WT……………………...50 Figure 11 Population of the four types of unfolding patterns in S15WT……………51 Figure 12 Force-extension patterns of S15mPK in 20 mM MgCl2………………….52 Figure 13 Distribution of the first unfolding force for S15mPK…………………….53 Figure 14 The PK unfolding transition processed at different rates…………………54 Figure 15 Force-extension patterns of S15mP/G in 20 mM MgCl2…………………55 Figure 16 The force-extension unfolding curves of the S15mH/G………………….56 Figure 17 The refolding curves of the five RNA constructs…………………………57 Figure 18 Folding and unfolding of the transition patterns………………...………..58 Figure 19 The model for the unfolding pathway ……………………………………59 Figure 20 Predicted secondary structure by Mfold for S15mPK and S15mP/G…….60 | |
| dc.language.iso | en | |
| dc.subject | 轉譯調控 | zh_TW |
| dc.subject | rpsO 信使核醣核酸 | zh_TW |
| dc.subject | 結構重組 | zh_TW |
| dc.subject | 單分子 | zh_TW |
| dc.subject | 光鉗 | zh_TW |
| dc.subject | optical tweezers | en |
| dc.subject | translational regulation | en |
| dc.subject | rpsO mRNA | en |
| dc.subject | structural rearrangement | en |
| dc.subject | single-molecule | en |
| dc.title | 以單分子研究 rpsO 基因 5’端未轉譯區的 RNA 結構重組 | zh_TW |
| dc.title | Single-Molecule Study of Structural Rearrangement of the rpsO 5’-UTR mRNA | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 100-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 張功耀,范秀芳 | |
| dc.subject.keyword | 轉譯調控,rpsO 信使核醣核酸,結構重組,單分子,光鉗, | zh_TW |
| dc.subject.keyword | translational regulation,rpsO mRNA,structural rearrangement,single-molecule,optical tweezers, | en |
| dc.relation.page | 60 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2012-08-03 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 分子與細胞生物學研究所 | zh_TW |
| 顯示於系所單位： | 分子與細胞生物學研究所 | |
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