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研究生: 謝書府
Hsieh, Shu-fu
論文名稱: 藉次微米界面構造侷限效應操控單分子DNA之研究:以電荷動力方法實現長鏈DNA分子之熵致捕捉、分子梳、及動態組裝之新微流體平台
Electrokinetic Manipulation of Single-Molecule Polymers within Submicron Interfacial Confinement : A New Microfluidic Platform for Entropic Trapping, Molecular Combing, and Dynamic Assembly of Long DNA Chains
指導教授: 魏憲鴻
Wei, Hsien-hung
學位類別: 碩士
Master
系所名稱: 工學院 - 化學工程學系
Department of Chemical Engineering
論文出版年: 2008
畢業學年度: 96
語文別: 中文
論文頁數: 167
中文關鍵詞: 自組織行為侷限效應界面薄膜電動力學操控DNADNA拉伸熵致捕捉分子梳微流體
外文關鍵詞: electrokinetic manipulations of DNA, DNA stretching, interfacial confinement, microfluidic, entropic trapping, self organization, molecular combing
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  • 本論文主要探討如何運用一個新的微流體平台,來實現各種電荷動力方法操控單分子DNA,本實驗利用兩相不互溶的流體在微流道中產生一個扁長型液珠使其大小幾乎貼近微流道管壁,而另一相流體則存在於此液珠與管壁表面之間形成了一個具有侷限效應的界面薄膜,其阻礙效應可迫使長鏈DNA分子產生形變。
    在外加電場的作用下配合此薄膜效應,使本實驗不僅實現了DNA分子之熵致捕捉、拉伸行為、以及DNA分子由油珠入口鑽入薄膜內的動態行為,更發現了DNA受到玻璃表面的界面活性劑影響,造成一種類似船錨般鉤附在界面活性劑疏水端的現象,在電場的作用下DNA在表面上進行一連串短暫接觸、拉伸、脫附、收縮的現象,因為DNA隨著其分子大小,與界面活性劑接觸的程度不同,所以不同DNA分子其遷移率隨著電場改變的程度也不同,因此提供了一個可用來分離DNA的可能方法。除此之外當玻璃表面上界面活性劑的吸附密度增加時,更形成了DNA分子梳,除去電場後,DNA分子間受到遠距的絮凝作用,而在表面上形成多個DNA分子聚集團,以至於吾人能夠觀察到DNA自身的組織行為,爾後更因為一開始並排拉伸的DNA在收縮鬆弛的過程中有橫向交聯的原故,使多個DNA分子聚集團在平行於電場的方向形成DNA分子束。除此之外我以直流電將DNA注入底層薄膜後,改以交流電場作用,發現DNA於油珠底層薄膜內存在一淨速度往其載入的反方向移動,更有類似大分子DNA在凝膠中延展纏繞於孔間隙的情形。以上各種DNA操控皆能在此次微米薄膜平台內達成。

    This thesis focuses on a new microfluidic platform capable of achieving a diversity of electrokinetic manipulations of DNA at the single-molecule level. The strategy invokes a submicron film between a closely fitting slug of the second fluid and the channel surface, creating an interfacial confinement to render conformation changes of a flexible DNA chain. I not only demonstrate that DNA molecules within the film can undergo entropic trapping, stretching, and translocation under the actions of an electric field, but also find the unique cyclic stick-slip behavior of the DNA motion with field and size dependent mobility due to interim anchoring between the DNAs and the surface surfactants, which has potential applications to on-chip DNA separation. In addition, with a dynamic template created by dense surface surfactant crowds, molecular combing and self organization of elongated DNA chains are also illustrated for the first time. In the latter case, DNAs can exhibit long-range flocculation or even develop to mesoscale bundles by the crosslink between the stretched chains. I also observe how DNAs respond to ac fields after being injected into the film with a dc field. I find, curiously, that the DNAs not only exhibit net motion toward the injection end but also show reptation behavior during its journey.
    All these findings suggest new paradigms for controlling the motion of DNA within submicron confinement.

    摘要……………………………………………………………i Abstract………………………………………………………ii 致謝……………………………………………………………iii 目錄……………………………………………………………iv 表目錄…………………………………………………………viii 圖目錄…………………………………………………………ix 符號說明………………………………………………………xix 第一章 緒論……………………………………………………1 1.1 研究背景……………………………………………………1 1.2 文獻回顧……………………………………………………2 1.2.1 電泳分離DNA之應用………………………………………2 1.2.2 DNA拉伸;DNA分子梳之研究……………………………4 1.3 研究動機……………………………………………………6 第二章 基本原理 ………………………………………………12 2.1電雙層(Electrical double layer)………………………12 2.2 電泳(electrophoresis)…………………………………14 2.3電滲流(Electro-osmosis, EO)……………………………15 2.4 DNA高分子特性(Static Properties of DNA Polymers)16 2.5 DNA分子電泳…………………………………………………18 2.6 DNA分子結構……………………………………………………19 2.7界面活性劑………………………………………………………20 第三章 微流道製作與組裝…………………………………………32 3.1 光罩設計…………………………………………………………32 3.2 光微影 (Photolithography) 製程……………………………32 3.2.1 晶片清洗………………………………………………………32 3.2.2 塗佈光阻 (Spin Coat)………………………………………33 3.2.3 軟烤 (Soft Bake)……………………………………………34 3.2.4 曝光 (Exposure)……………………………………………35 3.2.5 曝後烤 (Post Expose Bake)…………………………………36 3.2.6 顯影 (Development)…………………………………………37 3.2.7 硬烤 (Hard Bake)……………………………………………37 3.2.8 測量厚度………………………………………………………38 3.3 微流道製作………………………………………………………38 3.3.1 材料……………………………………………………………38 3.3.2 微流道模型製作………………………………………………38 3.4 微流道裝置組裝…………………………………………………39 3.4.1 接合……………………………………………………………39 3.4.2 管件組裝………………………………………………………41 3.4.3 PDMS表面改質…………………………………………………41 3.5 實驗設備…………………………………………………………42 第四章 以電荷動力方法結合次微米界面構造侷限效應操控單分子DNA…51 4.1 實驗………………………………………………………………52 4.1.1 微流道裝置……………………………………………………52 4.1.2 實驗溶液………………………………………………………53 4.1.3 硬體架構………………………………………………………55 4.1.4 實驗步驟………………………………………………………55 4.1.5相關實驗細節……………………………………………………57 4.1.6 影像處理軟體與拍攝…………………………………………58 4.2實驗觀測與記錄……………………………………………………62 4.2.1 DNA分子於薄膜入口處的運動情形與進入薄膜所需之最小電壓(臨界電壓)之測量62 4.2.2 DNA於扁長型油珠薄膜內的運動行為之觀測…………………63 4.2.3在外加電場下DNA於微流道中速度之測量……………………64 4.3實驗結果與討論……………………………………………………64 4.3.1臨界電場與DNA進入油珠底層薄膜之實驗結果………………64 4.3.2 DNA分子於薄膜入口處的運動情形及拉伸行為………………68 4.3.3 DNA分別於扁長型油珠底層薄膜與微流道中之運動行為實驗結果………………………………………………………………………70 4.3.4 DNA於扁長型油珠底層薄膜運動行為之理論推導…………72 4.3.5 界面活性劑的作用與影響……………………………………76 4.4結論………………………………………………………………79 第五章 以氧電漿改質玻璃表面,結合次微米界面與電荷動力方法,實現DNA分子梳、及動態組裝…………112 5.1 實驗………………………………………………………………113 5.1.1 實驗步驟………………………………………………………113 5.1.2相關實驗細節…………………………………………………113 5.2實驗觀測與記錄…………………………………………………114 5.3實驗結果與討論…………………………………………………115 5.3.1結合氧電漿改質玻璃表面,DNA於外加電場下在扁長型油珠薄膜內運動行為之結果………………………………………………115 5.3.2 高電場時在扁長型油珠薄膜內T4 DNA之可逆性分子梳……116 5.3.3 次微米薄膜內DNA的動態分子組裝…………………………118 5.4結論………………………………………………………………120 第六章 利用電泳方式驅動DNA進入次微米界面薄膜層後,於交流電場下之DNA動態行為探討…………………………………………130 6.1 實驗………………………………………………………………130 6.1.1硬體架構………………………………………………………130 6.1.2 實驗步驟………………………………………………………131 6.1.3相關實驗細節…………………………………………………132 6.2實驗觀測與記錄…………………………………………………132 6.2.1交流電場下,DNA於油珠底層薄膜之運動行為觀測…………132 6.2.2 結合氧電漿改質玻璃表面,於交流電場下,DNA於油珠底層薄膜之運動行為觀測……………………………………………………133 6.3實驗結果與討論…………………………………………………134 6.3.1 交流電場下,DNA於油珠底層薄膜運動行為之結果………134 6.3.2 結合氧電漿改質玻璃表面,在交流電場下,DNA於油珠底層薄膜運動行為之結果…………………………………………………135 6.4結論………………………………………………………………136 第七章 結論、未來展望……………………………………………144 參考文獻……………………………………………………………147 附錄A…………………………………………………………………152 附錄B…………………………………………………………………156 附錄C…………………………………………………………………160 附錄D…………………………………………………………………163 附錄E…………………………………………………………………164 自述…………………………………………………………………167

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