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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 謝之真(Chih-Chen Hsieh) | |
dc.contributor.author | Hou-Jun Guo | en |
dc.contributor.author | 郭厚均 | zh_TW |
dc.date.accessioned | 2021-06-15T11:15:01Z | - |
dc.date.available | 2016-08-25 | |
dc.date.copyright | 2016-08-25 | |
dc.date.issued | 2016 | |
dc.date.submitted | 2016-08-19 | |
dc.identifier.citation | 1. Odijk, T., POLYELECTROLYTES NEAR THE ROD LIMIT. Journal of Polymer Science Part B-Polymer Physics, 1977. 15(3): p. 477-483.
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Marsh, D., Lateral pressure profile, spontaneous curvature frustration, and the incorporation and conformation of proteins in membranes. Biophysical Journal, 2007. 93(11): p. 3884-3899. 15. Gruner, S.M., Intrinsic Curvature Hypothesis for Biomembrane Lipid-Composition - a Role for Nonbilayer Lipids. Proceedings of the National Academy of Sciences of the United States of America, 1985. 82(11): p. 3665-3669. 16. Israelachvili, J.N., Intermolecular & Surface Forces. 1985. 17. Kumar, V.V., Complementary Molecular Shapes and Additivity of the Packing Parameter of Lipids. Proceedings of the National Academy of Sciences of the United States of America, 1991. 88(2): p. 444-448. 18. Sackmann, E., Supported membranes: Scientific and practical applications. Science, 1996. 271(5245): p. 43-48. 19. Tamm, L.K. and H.M. McConnell, Supported phospholipid bilayers. Biophys J, 1985. 47(1): p. 105-13. 20. Rawicz, W., et al., Effect of chain length and unsaturation on elasticity of lipid bilayers. 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Annual Review of Physical Chemistry, Vol 62, 2011. 62: p. 483-506. 32. Kamal, M.M., et al., Measurement of the membrane curvature preference of phospholipids reveals only weak coupling between lipid shape and leaflet curvature. Proceedings of the National Academy of Sciences of the United States of America, 2009. 106(52): p. 22245-22250. 33. Chan, E.Y., et al., DNA mapping using microfluidic stretching and single-molecule detection of fluorescent site-specific tags. Genome Research, 2004. 14(6): p. 1137-1146. 34. R&D, J., Measuring Twisting Modulus of DNA - Predicted Effects of Local Conformational Coupling and External Restraints on the Torsional Properties of Single DNA Molecules 2007. 35. Nazari, Z.E. and L. Gurevich, Controlled deposition and combing of DNA across lithographically defined patterns on silicon. Beilstein Journal of Nanotechnology, 2013. 4: p. 72-76. 36. Lee, C.H. and C.C. Hsieh, Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations. Biomicrofluidics, 2013. 7(1). 37. Douville, N., D. Huh, and S. Takayama, DNA linearization through confinement in nanofluidic channels. Analytical and Bioanalytical Chemistry, 2008. 391(7): p. 2395-2409. 38. Hochrein, M.B., et al., DNA molecules on periodically microstructured lipid membranes: Localization and coil stretching. Physical Review E, 2007. 75(2). 39. 謝明勳, 於脂雙層上拉伸DNA與其基因圖譜應用之研究. 2014, 國立台灣大學化學工程研究所. 40. Neuman, K.C. and A. Nagy, Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nature Methods, 2008. 5(6): p. 491-505. 41. Zohar, H., et al., Peptide Nucleic Acids as Tools for Single-Molecule Sequence Detection and Manipulation. Nano Letters, 2010. 10(11): p. 4697-4701. 42. 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. 43. Schwartz, D.C. and A. Samad, Optical mapping approaches to molecular genomics. Current Opinion in Biotechnology, 1997. 8(1): p. 70-74. 44. Lee, H.E. and C.C. Hsieh, Using Nick-Labeling Technique to Perform Rapid DNA Optical Mapping on DNA Unravelled on Patterned Lipid Bilayers. 45. Iliafar, S., D. Vezenov, and A. Jagota, In-plane force-extension response of a polymer confined to a surface. European Polymer Journal, 2014. 51: p. 151-158. 46. Ando, T., T. Uchihashi, and T. Fukuma, High-speed atomic force microscopy for nano-visualization of dynamic biomolecular processes. Progress in Surface Science, 2008. 83(7–9): p. 337-437. 47. Leonenko, Z.V., et al., Lipid Phase Dependence of DNA−Cationic Phospholipid Bilayer Interactions Examined Using Atomic Force Microscopy. Langmuir, 2002. 18(12): p. 4873-4884. 48. Suzuki, Y., M. Endo, and H. Sugiyama, Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures. Nat Commun, 2015. 6. 49. Suzuki, Y., et al., Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface. Journal of the American Chemical Society, 2014. 136(5): p. 1714-1717. 50. Xiao, H., Introduction to Semiconductor Manufacturing Technology 3/E. 全華圖書股份有限公司: Taiwan. 51. Harries, D., S. May, and A. Ben-Shaul, Curvature and charge modulations in lamellar DNA-lipid complexes. Journal of Physical Chemistry B, 2003. 107(15): p. 3624-3630. 52. Kollmitzer, B., et al., Monolayer spontaneous curvature of raft-forming membrane lipids. Soft Matter, 2013. 9(45): p. 10877-10884. 53. Allende, D., S.A. Simon, and T.J. McIntosh, Melittin-induced bilayer leakage depends on lipid material properties: Evidence for toroidal pores. Biophysical Journal, 2005. 88(3): p. 1828-1837. 54. Kooijman, E.E., et al., Spontaneous curvature of phosphatidic acid and lysophosphatidic acid. Biochemistry, 2005. 44(6): p. 2097-2102. 55. Fuller, N. and R.P. Rand, The influence of lysolipids on the spontaneous curvature and bending elasticity of phospholipid membranes. Biophysical Journal, 2001. 81(1): p. 243-254. 56. Kučerka, N., S. Tristram-Nagle, and J.F. Nagle, Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains. The Journal of membrane biology, 2006. 208(3): p. 193-202. 57. Koltover, I., T. Salditt, and C. Safinya, Phase diagram, stability, and overcharging of lamellar cationic lipid–DNA self-assembled complexes. Biophysical Journal, 1999. 77(2): p. 915-924. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/49064 | - |
dc.description.abstract | 我們開發出具有低成本、操作容易等優勢的新型DNA基因圖譜分析平台,其原理為在具週期性的溝槽結構之基材上鋪設帶正電之脂雙層,使帶負電的DNA吸附於脂雙層上,並於自發性地於溝槽夾角之根部伸長呈一直線,使我們能夠直接標定DNA上的特定序列。我們已經在此平台上成功地使用缺口標定法產生基因圖譜。
為了能進一步提升對此系統之瞭解與掌控,我們希望能了解DNA沿著溝槽夾角根部自發拉伸之機制。DNA能自發拉伸顯示在夾角處存在一位能井,此位能井來自於DNA和正電脂質之靜電作用力,其可能成因有二: (1)正電脂質因立體效應而在夾角處聚集;(2)幾何效應的影響,即DNA在彎曲處能感應到較多正電荷。為了探討此一機制,我們使用三組不同脂質進行拉伸實驗: (A)DOPC/DOTAP,(B)DOPC/EPC,(C)DOPE/EPC。實驗結果顯示,立體效應與幾何效應的影響同時存在,在(A)、(B)組中帶正電脂質與電中性脂質親水端差距不大的情形下,幾何效應使DNA在帶有低正電比率的脂雙層上即可得到高DNA拉伸率;但在(C)組親水端差距較大的情形下,立體效應的影響使得即使在高正電比率的脂雙層上,DNA拉伸率仍然不高。 由於幾何效應的影響在文獻中未被提到,因此我們以Possion equation推導DNA在側壁夾角處的靜電位能,發現由幾何效應所產生的電位能差足夠提供DNA拉伸時的商損失。另外,我們也從理論上估計在(A)(B)(C)中正電脂質在側壁夾角處與平面處之分布情形,發現由脂質形狀所引發的濃度差異雖不大,但結合幾何效應的影響後,已足夠左右DNA的拉伸型態,這也解釋了我們在實驗中觀察到的現象。 最後我們希望以原子力顯微鏡量測DNA在側壁夾角拉伸的侷限寬度,並與de Gennes 和Odijk的理論比較。然而疏水端含雙鍵的脂雙層在液相時橫向擾動太快,使DNA無法以一般頻率的探針測得,對此我們希望藉由更換脂質,使脂雙層在常溫下為膠凝相,並能固定住DNA,此實驗仍有待進一步之研究。 | zh_TW |
dc.description.abstract | We have recently developed a DNA optical gene mapping platform. The working principle of the platform relies on the phenomenon that DNA can be adsorbed and spontaneously extended along a groove covered with cationic lipid bilayers. The physical gene map can then be readily obtained using nick-translating method.
This new platform has great potential because of its low cost and easy operation; however, the reason why DNA can spontaneously extend along the grooves is not clear and it has to be investigated in order to optimize the platform. Since DNA extends only along the grooves, it suggests there exists an electrostatic energy well for DNA. Two possible sources of this well are postulated: (1) the steric effect drives cationic lipids to aggregate on curved surface, (2) the geometry effect allows DNA to interact with more cationic lipids on the curved surface. In order to examine our postulations, we observed DNA behavior on three sets of lipid bilayers (A) DOPC/DOTAP, (B) DOPC/EPC and (C) DOPE/EPC, in which the ratio of the area of the headgroup to that of the tail varies gradually from larger than one to smaller than one. The experimental results show both the streic and the geometry effect exist. However, the geometry effect is always in favor of DNA extension while the steric effect can either enhance or undermine the phenomenon. We have also investigated the effect of the concentration of the positively charged lipids and found higher concentration always help DNA extend. In order to quantify the geometry effect, we have derived the electrostatic potential of DNA on curved surface and found the theoretical prediction is in quantitative agreement with the experimental results. We have also calculated lipid distribution due to steric effect and found that a modest variation of lipid concentration in conjunction with the geometry effect can lead to drastic change on DNA extension. Last but not least, we want to measure the width of the DNA confinement using atomic force microscopy and compare our results with the prediction between DNA extension and the confinement width proposed by de Gennes and Odijk. However, since the lateral diffusion of the lipid bilayer is too fast, we cannot find DNA on lipid bilayer using normal AFM probes. We plan to solve this problem in the future by employing lipids with transition temperatures higher than the room temperature so that lipid bilayer can remain in gel phase during experiments. | en |
dc.description.provenance | Made available in DSpace on 2021-06-15T11:15:01Z (GMT). No. of bitstreams: 1 ntu-105-R03524087-1.pdf: 4745661 bytes, checksum: 3deb32d0e54e0e4e11d51a97ebdf88e7 (MD5) Previous issue date: 2016 | en |
dc.description.tableofcontents | 致謝 1
摘要 I Abstract III 目錄 V 圖目錄 VII 表目錄 XIII 第一章 緒論 1 1.1 前言 1 1.2 研究動機與目的 2 第二章 文獻回顧 3 2.1 DNA介紹 3 2.1.1 DNA的結構 3 2.1.2 DNA的高分子性質 5 2.1.3 DNA於侷限環境 7 2.2 脂質 10 2.2.1 脂質的基本性質 10 2.2.2 脂質的自組裝行為(Self-assembly) 11 2.2.3 支托脂雙層(Supported Lipid Bilayer) 16 2.2.4 脂雙層於彎曲表面之排序(Sorting) 19 2.3 DNA物理圖譜 23 2.3.1 直接線性分析法(Direct Linear Analysis, DLA) 24 2.3.2 DNA 標定技術(DNA Labeling) 25 2.3.3 DNA 拉伸技術(DNA Stretching) 26 2.3.1 脂雙層拉伸法(DNA on lipid bilayer) 28 2.4 研究現況 31 2.4.1 DNA拉伸 31 2.4.2 DNA標定 34 2.5 研究理念 36 第三章 實驗設計構想 38 3.1 DNA於側壁夾角之靜電位能 38 3.2 在二維空間下伸長量與DNA之侷限寬度之關係 43 第四章 實驗設備與步驟 47 4.1 儀器設備 47 4.2 實驗藥品 50 4.3 實驗方法與步驟 52 4.3.1 圖案玻片之製作[50] 52 4.3.2 脂質溶液配製 56 4.3.3 脂雙層之架設 56 4.3.4 DNA溶液配置 57 第五章 實驗結果分析與討論 60 5.1 DNA於側壁夾角聚集拉伸之機制 60 5.1.1 在不同組成之脂雙層上拉伸DNA 60 5.1.2 DNA在側壁夾角受幾何效應影響之算式推導 64 5.2 以AFM量測在脂雙層上拉伸的DNA 80 5.2.1 以AFM量測玻璃基材上之DOPC/DOTAP脂雙層 80 第六章 結論 89 參考文獻 91 | |
dc.language.iso | zh-TW | |
dc.title | DNA 於脂雙層上自發伸展機制及侷限行為之研究 | zh_TW |
dc.title | Research of DNA Stretching Mechanism on Lipid Bilayer and Its Behavior Under Confinement | en |
dc.type | Thesis | |
dc.date.schoolyear | 104-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 戴子安(Chi-An Dai),王勝仕(Steven S.-S. Wang),康敦彥(Dun-Yen Kang) | |
dc.subject.keyword | DNA拉伸,脂質,曲面, | zh_TW |
dc.subject.keyword | DNA stretching,Lipids,Curved surface, | en |
dc.relation.page | 95 | |
dc.identifier.doi | 10.6342/NTU201603431 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2016-08-21 | |
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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