臺灣博碩士論文加值系統

本論文的內容是研究DNA在奈米結構中的行為。在奈米/微米流體系統中，表面對體積比遠較一般系統大，因此必須考慮表面的電學效應。另外、DNA本身的形狀受到邊界的限制而產生變化。此兩者的交互影響下使DNA在奈米結構裡的行為與自由溶液中有明顯的不同。
我們的研究分為兩個部分：多價正離子誘導DNA自發凝聚及電場對奈米結構中DNA操控。當多價正離子存在溶液中時，DNA會從自由延伸擾動的長鏈分子凝縮成極小超環形或柱形，此現象在過去已經有相當多的理論與實驗，但卻缺乏奈米結構對DNA凝縮的影響。在我們的實驗中我們發現DNA凝縮的現象會隨著邊界限制改變，限制越強時凝縮的時間就會增加。我們認為增加的部分是來自於在de Gennes regime中鬆弛時間的增加導致凝縮需要較長的時間。但其中應該還牽涉了更多其他的效應，必須藉由更進一步的研究來確認。
第二個部分是有關奈米結構中的DNA在電場下的運動行為。自由溶液中、DNA受到電場時的行為可以完全由電泳理論決定。但在奈米結構中DNA在電場下的運動遠較前者複雜。此時，EOF、濃度極化、表面電導還有許多相關的效應都必須加以考慮。我們在這部份的工作就是研究奈米結構中DNA在電場下的運動行為，並且整理各個尺度下的主要影響的因子。此外、我們在研究的過程中發現了過去所沒有發現的DNA回流現象。

This thesis is focus on the studying of DNA behaviors in nanoconfinement. In nano/micro fluidic systems, the surface to volume ratio becomes too large to neglect the electrokinetics on the surface. And in nanoconfinement, DNA is forced to be confined to a limit region. This changes the conformation and transport mechanism of DNA and generates lots of novel phenomena.
We studied two separate parts: DNA condensation induced by multivalent ions and DNA transport induced by electric field in nanostructures. DNA condensation is a well-known phenomenon. The free-coil-chain-like conformation of DNA transforms to condensed toroid or rod in the existence of multivalent ions. In our experiment, we studied the influence of confinement to DNA condensation. We found that DNA condensation process is slower in strong confinement than in free solution in de Gennes regime. This can be partly explained by the increasing relaxation time in strong confinement.
The second part is DNA transport in nanostructures induced by electric field. In free solutions, DNA transport under electric field can be fully explained by electrophoresis. Though in nanostructures, DNA transport is more complicated than that in free solutions. EOF, concentration polarization, surface conductance, DNA trapping, and lots of other effect should be taken into considerations. We categorize DNA transport in nanostructures induced by electric field and try to clarify the main factors that participate in. In free solutions or microchannels, DNA transport is dominated by electrophoresis. However, in nanostructures EOF may strong enough to dominate the transport direction. And in stronger confinement, we have to take EOF of the second kind and concentration polarization into considerations.

Certificate of Approval…………………………………………… i
Acknowledgement…………………………………………………... ii
Abstract………………………………………………………………iii
List of Figures……………………………………………………………… v
Chapter 1. Introduction………………………………………………1
1.1 Micro/Nano Fluidic Systems and Single DNA Experiments in
Nanostructures……………………………………………………....1
1.2 Motivation………………………………………………………2

Chapter 2. Theories…………………………………………………4
2.1 Static Model for DNA…………………………………………4
Models of Free Polymer Chain………………………………………4
Excluded Volume Effect………………………………………………7
Radius of Gyration…………………………………………………….9
Static Scaling in Quasi-2D Nanoslits……………………………10
2.2 DNA Condensation by Multivalent Counterion-……………12
Statical Analysis of Polymer Condensation……………………13
Forces in DNA Condensation…………………………………………15
2.3 Microfluidic Electrophoresis & Ions transportation inside nanostructures....................................20
Poisson–Boltzmann equation……………………………………21
Electrical Double Layer……………………………………………22
Electrophoresis………………………………………………………25
Electroosmic flow……………………………………………………27
EOF of the second kind………………………………………………28
Concentration Polarization ………………………………………29
DNA Self Trapping in Nanofluidic Device………………………32

Chapter 3. System of Experiment………………………35
3.1 DNA sample and buffer solution preparation………………35
3.2 Chips Fabrications………………………………………………36
3.3 System Alignment…………………………………………………37
3.4 Data Analysis……………………………………………………38

Chapter 4. DNA Condensation with Multivalent Ions40
4.1 Experiment Method……………………………………………41
4.2 Result and Discussion…………………………………………42

Chapter 5. DNA Transport in Nanostructures induced by elextric field……....................................50
5.1 Chips Design………………………………………………………51
5.2 Result and Discussion…………………………………………52

Chapter 6. Summary……………………………………………………68
Reference………………………………………………………………70
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