原子力顯微鏡(AFM)能在氣相、真空、及接近生理條件的液相中直接進行表面單分子的觀測。但樣品分子被固定後，其結構是否與自然狀態相關，頗令人質疑。
本研究針對雲母片表面進行化學修飾，利用精胺(spermine)大大提高了基板表面吸附DNA的能力。運用聚合分子鏈統計分析理論(statistical polymer chain analysis)，以三種不同長度的線型DNA分子，根據AFM影像分別作分子輪廓總長(contour length, L)及未端兩點距離(end-to-end distance, R)的測量，以<R2>與L之相關性推知影像中的DNA分子表現的是3D立體捕捉態構型(three-dimensional trapped configuration)，而非分子在2D空間重新建立平衡後的結構。另外，藉改變DNA樣品液滴在雲母片上乾燥的時間，所造成基板吸附分子數目的變化，配合不可逆擴散運動模型得到了分子由液相到達表面輸送過程之擴散係數。
在拓樸異構&#37238;(topoisomerase)與催化DNA分子反應實驗中，AFM明顯辨識出DNA分子在拓樸構形上的轉化，甚至直接看到解旋機制中拓樸&#37238;分子與雙股DNA中一條單股的作用。

原子力顯微鏡(AFM)能在氣相、真空、及接近生理條件的液相中直接進行表面單分子的觀測。但樣品分子被固定後，其結構是否與自然狀態相關，頗令人質疑。
本研究針對雲母片表面進行化學修飾，利用精胺(spermine)大大提高了基板表面吸附DNA的能力。運用聚合分子鏈統計分析理論(statistical polymer chain analysis)，以三種不同長度的線型DNA分子，根據AFM影像分別作分子輪廓總長(contour length, L)及未端兩點距離(end-to-end distance, R)的測量，以<R2>與L之相關性推知影像中的DNA分子表現的是3D立體捕捉態構型(three-dimensional trapped configuration)，而非分子在2D空間重新建立平衡後的結構。另外，藉改變DNA樣品液滴在雲母片上乾燥的時間，所造成基板吸附分子數目的變化，配合不可逆擴散運動模型得到了分子由液相到達表面輸送過程之擴散係數。
在拓樸異構&#37238;(topoisomerase)與催化DNA分子反應實驗中，AFM明顯辨識出DNA分子在拓樸構形上的轉化，甚至直接看到解旋機制中拓樸&#37238;分子與雙股DNA中一條單股的作用。

目錄
摘要 i
目錄 ii
圖表目錄 v

第壹章、緒論 1
1-1研究背景 1
1-2核酸 1
1-3 DNA拓樸結構 4
1-4原子力顯微鏡 7
1-5原子力顯微鏡在生物學上的應用 8
1-6理論背景 10
1-6-1 DNA分子沉積 10
1-6-2聚合分子鏈統計分析理論
(statistical polymer chain analysis) 11
1-7研究動機 13
第貳章、實驗 14
2-1實驗儀器 14
2-2原子力顯微鏡原理 14
2-2-1 Contact(接觸)及Tapping mode(輕敲) 16
2-3氣、液相掃描 17
氣相AFM的操作步驟 18
液相AFM的操作步驟 20
2-4實驗材料 20
<a>基板 20
<b> DNA樣品 21
<c> DNA的生物緩衝液 21
2-5實驗流程 24
2-5-1樣品配製 24
滅菌水 24
微量離心管(microtube)、吸管尖(tip)與樣品瓶之滅菌 24
精胺(spermine-)與亞精胺(spermindine)-Mica的製備 25
AP-mica的製備 25
2-5-2實驗流程 26
DNA觀測 26
擴散實驗 27
拓樸&#37238;實驗 27
第參章、結果與討論 28
3-1雲母基板(mica substrate) 28
3-2氣相AFM觀察雲母基板上的DNA分子 29
3-3雲母表面之化學修飾 29
3-4 Spermine及Spermidine濃度對固定DNA能力的探討 32
3-5溶液中DNA的傳輸：擴散吸附過程 37
3-6氣相AFM之DNA分子成像 40
3-7聚合分子鏈統計分析理論(statistical polymer chain analysis) 41
3-8 DNA超螺旋(supercoiling) 46
3-9 DNA超螺旋度(supercoil density)的量測 51
3-10拓樸異構&#37238; 53
3-11 DNA分子構型之轉化過程 64
第肆章、結論 71
參考文獻 74

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