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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 謝之真 | |
| dc.contributor.author | Szu-Chi Huang | en |
| dc.contributor.author | 黃思齊 | zh_TW |
| dc.date.accessioned | 2021-06-15T07:09:11Z | - |
| dc.date.available | 2015-10-31 | |
| dc.date.copyright | 2010-10-31 | |
| dc.date.issued | 2010 | |
| dc.date.submitted | 2010-10-21 | |
| dc.identifier.citation | 第七章 參考文獻
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Larson, J.W., et al., Single DNA molecule stretching in sudden mixed shear and elongational microflows. Lab on a Chip, 2006. 6(9): p. 1187-1199. 15. Perkins, T.T., D.E. Smith, and S. Chu, Single polymer dynamics in an elongational flow. Science, 1997. 276(5321): p. 2016-2021. 16. Randall, G.C., K.M. Schultz, and P.S. Doyle, Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices. Lab on a Chip, 2006. 6(4): p. 516-525. 17. Hsieh, C.C. and P.S. Doyle, Studying confined polymers using single-molecule DNA experiments. Korea-Australia Rheology Journal, 2008. 20(3): p. 127-142. 18. Perkins, T.T., et al., Stretching of a Single Tethered Polymer in a Uniform-Flow. Science, 1995. 268(5207): p. 83-87. 19. Davenport, R.J., et al., Single-molecule study of transcriptional pausing and arrest by E-coli RNA polymerase. Science, 2000. 287(5462): p. 2497-2500. 20. Ferree, S. and H.W. Blanch, Electrokinetic stretching of tethered DNA. Biophysical Journal, 2003. 85(4): p. 2539-2546. 21. Perkins, T.T., et al., Relaxation of a single DNA molecule observed by optical microscopy. Science, 1994. 264(5160): p. 822-826. 22. Smith, S.B., Y.J. Cui, and C. Bustamante, Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science, 1996. 271(5250): p. 795-799. 23. Ladoux, B. and P.S. Doyle, Stretching tethered DNA chains in shear flow. Europhysics Letters, 2000. 52(5): p. 511-517. 24. Williams, M.C., et al., Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching. Biophysical Journal, 2001. 80(4): p. 1932-1939. 25. Michalet, X., et al., Dynamic molecular combing: Stretching the whole human genome for high-resolution studies. Science, 1997. 277(5331): p. 1518-1523. 26. Juang, Y.J., et al., Dynamics of single polymers in a stagnation flow induced by electrokinetics. Physical Review Letters, 2004. 93(26): p. 268105. 27. Tang, J. and P.S. Doyle, Electrophoretic stretching of DNA molecules using microscale T junctions. Applied Physics Letters, 2007. 90(22): p. 224103-224103-3. 28. Smith, D.E. and S. Chu, Response of flexible polymers to a sudden elongational flow. Science, 1998. 281(5381): p. 1335-1340. 29. Ronai, Z., et al., DNA analysis on electrophoretic microchips: Effect of operational variables. Electrophoresis, 2001. 22(2): p. 294-299. 30. Randall, G.C. and P.S. Doyle, Electrophoretic collision of a DNA molecule with an insulating post. Physical Review Letters, 2004. 93(5): p. 058102. 31. Heng, J.B., et al., Stretching DNA using the electric field in a synthetic nanopore. Nano Letters, 2005. 5(10): p. 1883-1888. 32. Yang, B., et al., Stretching and selective immobilization of DNA in SU-8 micro- and nanochannels. Journal of Vacuum Science & Technology B, 2007. 25(6): p. 2352-2356. 33. Riehn, R., et al., Restriction mapping in nanofluidic devices. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(29): p. 10012-10016. 34. Jo, K., et al., A single-molecule barcoding system using nanoslits for DNA analysis. Proceedings of the National Academy of Sciences of the United States of America, 2007. 104(8): p. 2673-2678. 35. Reisner, W., et al., Statics and dynamics of single DNA molecules confined in nanochannels. Physical Review Letters, 2005. 94(19): p. 196101. 36. Maier, B. and J.O. Radler, DNA on fluid membranes: A model polymer in two dimensions. Macromolecules, 2000. 33(19): p. 7185-7194. 37. Groves, J.T., N. Ulman, and S.G. Boxer, Micropatterning fluid lipid bilayers on solid supports. Science, 1997. 275(5300): p. 651-653. 38. Mennicke, U. and T. Salditt, Preparation of solid-supported lipid bilayers by spin-coating. Langmuir, 2002. 18(21): p. 8172-8177. 39. Olson, D.J., et al., Electrophoresis of DNA adsorbed to a cationic supported bilayer. Langmuir, 2001. 17(23): p. 7396-7401. 40. Mayer, L.D., M.J. Hope, and P.R. Cullis, Vesicles of Variable Sizes Produced by a Rapid Extrusion Procedure. Biochimica Et Biophysica Acta, 1986. 858(1): p. 161-168. 41. Macdonald, R.C., et al., Small-Volume Extrusion Apparatus for Preparation of Large, Unilamellar Vesicles. Biochimica Et Biophysica Acta, 1991. 1061(2): p. 297-303. 42. Avanti FAQ - When I initially prepare my lipids to form liposomes, do I have to place the lipids in a vacuum to remove the residual chloroform? . Available from: http://avantilipids.com/index.php?view=items&cid=5&id=17&option=com_quickfaq&Itemid=385. 43. Lin, P.K., et al., Static conformation and dynamics of single DNA molecules confined in nanoslits. Physical Review E, 2007. 76(1): p. 011806. 44. Lin, P.K., et al., One-Dimensional Dynamics and Transport of DNA Molecules in a Quasi-Two-Dimensional Nanoslit. Macromolecules, 2009. 42(5): p. 1770-1774. 45. Hochrein, M.B., et al., DNA localization and stretching on periodically microstructured lipid membranes. Physical Review Letters, 2006. 96(3): p. 038103. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/48700 | - |
| dc.description.abstract | 本論文的目的在於開發具有良好的DNA分子拉伸效果，製程相對簡單且成本低的拉伸平台。現行眾多拉伸DNA分子的方法中，以侷限拉伸法的拉伸均一度為最佳，由於其原理為透過將DNA分子侷限於狹窄的空間(如：奈米通道、奈米狹縫等)中，並利用DNA分子自身不相交疊的特性來促使其延展並拉伸，因此DNA分子的延展度將隨著侷限空間的縮小而增加，縮小侷限空間便隨之成為發展趨勢；但同時卻也帶來了製程上的困難。為了能於拉伸效果不變的前提下，發展出更為優秀的拉伸平台，我們以侷限拉伸法的原理做為基礎，衍伸出嶄新的DNA拉伸方法：帶狀侷限法。
帶狀侷限法的核心概念是將DNA分子侷限於奈米尺度的帶狀平面，由於DNA為帶負電的高分子，我們將目標訂為製作出數百奈米寬的正電帶狀平面；假設DNA分子位於直角坐標系中，數百奈米的圖形寬度與靜電力的吸引將各自對DNA分子進行X軸與Z軸方向的侷限，促使DNA分子僅能延Y軸方向延展來達到被拉伸的目的。 正電帶狀平面的核心建立技術，共可分為兩個部分，一為如何建立均勻平整的帶正電平面，二為帶狀圖形的建立：使帶電平面達到我們數百奈米的寬度需求。首先，我們以架設於蓋玻片上的正電脂雙層(lipid bilayer)做為帶正電平面，帶狀圖形的建立則依方法原理的不同，衍伸出兩種較奈米通道簡易的製程：側壁限制法與帶狀圖形限制法。 利用側壁限制法，DNA分子的平均延展度可達到0.56，拉伸效果約相等於長寬介於60nm至80nm的矩形奈米通道，此結果證明了側壁限制法除了製程上的優勢，更具有優秀的拉伸效果。另一方面，以300nm寬的帶狀圖形限制法所獲得的DNA分子延展度約為0.4，其目前結果雖仍不及側壁限制法，但卻具有較側壁限制法更大的改善空間。帶狀侷限法目前於拉伸效果上雖仍不能取代現有侷限拉伸法，但相信能為相關領域帶來新的思維與方向。 | zh_TW |
| dc.description.abstract | This thesis focuses on the development of a new platform that is capable of stretching DNA to a high degree while can be manufactured economically. Among current technologies for DNA stretching, confining DNA molecule in a nanochannel has been shown to provide the best stretching uniformity. “Confining DNA” means restricting DNA in a small space. Due to the excluded volume effects, DNA will extend more when the space becomes narrower. However, a reasonable DNA extension can only be achieved when the dimension of a nanochannel reduces to below 100nm, making such nanochannel expensive and difficult to produce. Inspired by the concept of confinement, we develop an alternative approach, called strip confinement, to stretch DNA molecule.
The core concept of strip confinement is to restrict DNA in a strip-shaped two-dimensional plane. The two-dimensional nature of the platform enhances the excluded volume effects, and therefore is more advantageous for the application of DNA stretching. Since DNA is negatively charged in physiological condition, the proposed platform is realized by creating parallel strips of positively charged lipid bilayer on a glass. The processes for manufacturing our platforms, including the creation of the patterned surface and the setup of lipid bilayer, are more economical than those for producing nanochannels. Based on our new approach, we investigate two different ways to stretch DNA, sidewall confinement and direct strip confinement. The former stretches DNA along its corner where the lipid density is highest, the latter stretches DNA along its axis. The average degree of DNA extension measured from a sidewall confinement is 0.56, close to that obtained from nanochannels with the width between 60nm to 80nm. The degree of DNA extension measured from a Direct strip confinement with 300nm in width is 0.4, a little lower than that of the former method. The results presented here are for proof-of-principle, and we expect that our devices based on the concept of strip confinement can be further improved for better performance and lower cost. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-15T07:09:11Z (GMT). No. of bitstreams: 1 ntu-99-R97524059-1.pdf: 14568589 bytes, checksum: 701ed7e8de4d4534fb06cad1407aae0b (MD5) Previous issue date: 2010 | en |
| dc.description.tableofcontents | 目錄
中文摘要…………………………………………………………………………… I 英文摘要…………………………………………………………………………… II 誌謝………………………………………………………………………………… III 表目錄……………………………………………………………………………… VI 圖目錄……………………………………………………………………………… VII 第一章 緒論………………………………………………………………………… 1 1.1 前言……………………………………………………………………………… 1 1.2 DNA分子結構與性質…………………………………………………………… 2 1.3現行DNA基因圖譜相關技術…………………………………………………… 5 1.3.1 限制酵素……………………………………………………………………… 5 1.3.2 藻膠電泳……………………………………………………………………… 6 1.3.3 聚合酵素鏈鎖反應…………………………………………………………… 7 1.3.4 DNA定序……………………………………………………………………… 8 1.4研究動機與目的………………………………………………………………… 10 第二章 文獻回顧…………………………………………………………………… 12 2.1 直接線性分析法………………………………………………………………… 12 2.1.1標定技術……………………………………………………………………… 12 2.1.2 DNA拉伸技術……………………………………………………………… 12 2.1.2.1 現行DNA拉伸技術……………………………………………………… 12 2.1.2.2 新型DNA拉伸技術：帶狀侷限法……………………………………… 20 2.2 帶狀侷限法……………………………………………………………………… 21 2.2.1 二維平面的建立……………………………………………………………… 22 2.2.2 帶狀圖形的建立……………………………………………………………… 25 第三章 實驗設備與步驟…………………………………………………………… 28 3.1 儀器設備………………………………………………………………………… 28 3.2 實驗藥品………………………………………………………………………… 29 3.3 實驗方法………………………………………………………………………… 30 3.3.1 DNA容易之製備……………………………………………………………… 30 3.3.2 脂雙層的架設………………………………………………………………… 31 3.3.3 帶狀圖形的建立……………………………………………………………… 36 3.3.3.1 側壁限制法………………………………………………………………… 36 3.3.3.2 帶狀圖形限制法…………………………………………………………… 44 第四章 實驗結果與討論…………………………………………………………… 50 4.1 側壁限制法……………………………………………………………………… 50 4.1.1 DNA分子拉伸結果與討論…………………………………………………… 50 4.1.2 結果比較……………………………………………………………………… 57 4.1.2.1 奈米通道…………………………………………………………………… 57 4.1.2.2 擬二維奈米狹縫…………………………………………………………… 59 4.1.2.3 微帶狀溝槽結構上之脂雙層……………………………………………… 61 4.2 帶狀圖形限制法………………………………………………………………… 63 第五章 結論………………………………………………………………………… 65 第六章 未來展望…………………………………………………………………… 67 第七章 參考文獻…………………………………………………………………… 67 表 目 錄 表2-1 現行DNA拉伸技術一覽表……………………………………………… 19 表2-2 帶狀侷限法的優點………………………………………………………… 21 圖 目 錄 Fig. 1-1. 核苷酸。…………………………………………………………………… 3 Fig. 1-2. 核酸鹼基。………………………………………………………………… 3 Fig. 1-3. 磷酸雙脂鍵與DNA股的共價結構。……………………………………… 3 Fig. 1-4. DNA鹼基配對；虛線代表氫鍵，dR = deoxyribose。…………………… 4 Fig. 1-5. DNA雙股螺旋結構示意圖。……………………………………………… 4 Fig. 1-6. DNA重複單位示意圖。…………………………………………………… 5 Fig. 1-7. 限制酵素切割序列示意圖。……………………………………………… 6 Fig. 1-8. 藻膠電泳裝置。…………………………………………………………… 6 Fig. 1-9. 聚合酵素鏈鎖反應原理示意圖。………………………………………… 7 Fig. 1-10. Maxam-Gilbert法原理示意圖。………………………………………… 8 Fig. 1-11. Sanger法原理示意圖。………………………………………………… 9 Fig. 1-12. 直接線性分析法示意圖。……………………………………………… 11 Fig. 2-1. 栓扯拉伸法原理示意圖。……………………………………………… 14 Fig. 2-2. 分子梳拉伸法原理示意圖。…………………………………………… 15 Fig. 2-3. 漸縮通道─流速分佈圖。……………………………………………… 16 Fig. 2-4. 漸縮通道─電位梯度分佈圖。………………………………………… 17 Fig. 2-5. DNA侷限狀態示意圖。………………………………………………… 18 Fig. 2-6. DNA二維侷限示意圖。………………………………………………… 20 Fig. 2-7. DNA 吸附於脂雙層表面。……………………………………………… 21 Fig. 2-8. 脂雙層基本結構。……………………………………………………… 22 Fig. 2-9. 使用旋轉塗佈法建立脂雙層。………………………………………… 23 Fig. 2-10. 不同種類與粒徑之脂球。……………………………………………… 24 Fig. 2-11. 使用脂球融合方法建立脂雙層。……………………………………… 24 Fig. 2-12. 側壁限制法原理示意圖。……………………………………………… 25 Fig 2-13. 直接帶狀圖形限制法示意圖。………………………………………… 26 Fig 2-14. 特徵尺度說明圖。……………………………………………………… 27 Fig 3-1. 脂雙層裝置完成示意圖。……………………………………………… 32 Fig. 3-2. 利用渦流攪拌器(Vortex)幫助氯仿揮發。……………………………… 32 Fig. 3-3. 多層脂球與單層脂球。………………………………………………… 33 Fig. 3-4.多餘脂質未完整除去的情形。…………………………………………… 35 Fig. 3-5. 側壁夾角說明圖。……………………………………………………… 36 Fig. 3-6. 側壁限制法製程原理示意圖。………………………………………… 38 Fig. 3-7. 光罩設計圖。…………………………………………………………… 39 Fig. 3-8. 光罩製作原理。………………………………………………………… 39 Fig. 3-9. 側壁夾角產生原理示意圖。…………………………………………… 42 Fig. 3-10. 側壁限制裝置示意圖。……………………………………………… 44 Fig. 3-11. 帶狀圖形限制法製程原理示意圖。………………………………… 46 Fig. 3-12. 直接帶狀圖形設計圖。……………………………………………… 47 Fig. 3-13. 直接帶狀圖形限制裝置示意圖。…………………………………… 49 Fig. 4-1. (a) DNA分子於三維空間（溶液中）的情形； (b) DNA分子於二維空間（脂雙層上）的情形。…………………… 50 Fig. 4-2. 於觀測時間內，DNA分子隨被吸附區域的不同而有不同的延展情形（圖中白色呈線狀的是묬-DNA分子，黑色部分為脂雙層，上下白色部分為S1813正光阻）。……………………………………………………………………………… 52 Fig. 4-3. 側壁夾角實測圖。……………………………………………………… 53 Fig. 4-4. 摺疊DNA分子展開圖。………………………………………………… 54 Fig.4-5. DNA分子長度量測說明圖。…………………………………………… 54 Fig. 4-6. 摺疊DNA分子展開過程圖。…………………………………………… 55 Fig. 4-7. DNA分子延展度結果統計圖（側壁限制法）。……………………… 56 Fig. 4-8. DNA分子經弱直流電場處理前後的平均延展度（側壁限制法）。… 57 Fig. 4-9. 側壁限制法V.S.奈米通道的DNA延展度比較圖。…………………… 59 Fig. 4-10. 文獻 [43] 裝置示意圖。……………………………………………… 60 Fig. 4-11. 側壁限制法V.S.奈米狹縫側壁的DNA延展度比較圖。…………… 61 Fig. 4-12. 微帶狀溝槽AFM結構圖。…………………………………………… 62 Fig. 4-13 DNA分子於微帶狀溝槽脂質層的拉伸情形。……………………… 63 Fig. 4-14. 黃金帶狀圖形SEM掃描圖。………………………………………… 64 Fig. 4-15. DNA分子於帶狀圖形限制裝置中的吸附情形。…………………… 65 | |
| dc.language.iso | zh-TW | |
| dc.subject | 側壁限制法 | zh_TW |
| dc.subject | 帶狀圖形限制法 | zh_TW |
| dc.subject | 拉伸DNA分子 | zh_TW |
| dc.subject | 脂雙層 | zh_TW |
| dc.subject | Stretch DNA molecule | en |
| dc.subject | lipid bilayer | en |
| dc.subject | strip confinement | en |
| dc.title | 於脂雙層上拉伸DNA之研究 | zh_TW |
| dc.title | Research of DNA stretching on lipid bilayer | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 99-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 廖英志,吳嘉文 | |
| dc.subject.keyword | 拉伸DNA分子,脂雙層,側壁限制法,帶狀圖形限制法, | zh_TW |
| dc.subject.keyword | Stretch DNA molecule,lipid bilayer,strip confinement, | en |
| dc.relation.page | 70 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2010-10-21 | |
| dc.contributor.author-college | 工學院 | zh_TW |
| dc.contributor.author-dept | 化學工程學研究所 | zh_TW |
| 顯示於系所單位： | 化學工程學系 | |
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