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論文中文名稱:評估蒽醌吡咯氧化還原嵌入型探針運用於電化學基因檢測 [以論文名稱查詢館藏系統]
論文英文名稱:Evaluation of Anthraquinone-Pyrrole Dyad Redox Intercalating Probes for Electrochemical Gene Detection [以論文名稱查詢館藏系統]
院校名稱:臺北科技大學
學院名稱:工程學院
系所名稱:化學工程與生物科技系化學工程博士班
畢業學年度:103
畢業學期:第二學期
中文姓名:林宥任
英文姓名:Yu-Jen Lin
研究生學號:102738053
學位類別:碩士
語文別:中文
口試日期:20150617
指導教授中文名:黃聲東
指導教授英文名:Sheng-Tung Huang
口試委員中文名:郭憲壽;高佳麟
中文關鍵詞:電化學聚合酶鏈鎖反應基因檢測氧化還原嵌入型探針蒽醌吡咯
英文關鍵詞:Electrochemical PCRgene detectionDNA intercalating probepyrroleanthraquinone
論文中文摘要:電化學即時定量聚合酶鏈鎖反應,是利用觀察嵌入型氧化還原探針在嵌入聚合酶鏈鎖反應所產生的擴增子造成電訊號之變化,來定量待測基因所具有之拷貝數。首先,我們設計並製備了一系列蒽醌吡咯衍生物(AP1、AP2及AP3)作為嵌入型氧化還原探針,並經由氫譜、碳譜及質譜多重確認其結構。接下來,探針與DNA的結合特異性我們藉由檢測其與小牛胸腺DNA之結合常數(Kb)、結合位置大小(s)及嵌入DNA前後擴散速率之改變(D),並與圓二色光譜做對照,證明探針確實具有良好的去氧核醣核酸結合特異性,且隨著探針上所具有之吡咯數目越多,其結合特異性越高。為確認探針應用於電化學即時定量聚合酶鏈鎖反應的可行性,我們緊接著對探針做了熱穩定性及反應抑制性之檢測。結果可見三個探針在30與50μM的濃度下都具有良好的熱穩定性質且不會對PCR反應造成抑制的效果。最後,我們將結合特異性最好的AP3實際應用於電化學定量聚合酶鏈鎖反應來檢測tpc序列,其最低偵測極限可達到103個拷貝數。因此我們提供了一系列新的嵌入型氧化還原探針並且將其實際運用至電化學即時定量聚合酶鏈鎖反應,達到方便且快速基因檢測之目的。
論文英文摘要:The electrochemical real-time quantitative PCR, a nucleic acid amplification method to quantify the initial copy number of target gene is a promising method for the monitoring of pathogenic DNAs in which redox probes are the signal revealing reporters. In the present work, a series of DNA intercalating redox probes (AP1, AP2 and AP3) based on anthraquinone-pyrrole derivatives have been designed and prepared and explored in real-time electrochemical PCR application. The structural aspects of these probes were characterized by 1H NMR, 13C NMR and mass spectroscopies, while electrochemical behavior of these compounds was derived from voltammetry. The cyclic voltammograms of these probes present the characteristic redox signals of anthraquinone. The electrochemical redox signal of these proves decreases exponentially with each amplification cycles indicating the efficient binding of double stranded amplicons with the probes. The DNA intercalating ability of these probes in terms of binding constant, binding site size and diffusion coefficient have been estimated and these parameters indicating that the probes have great ability to strongly bind to the calf thymus DNA. Notably, AP3 shows maximum DNA intercalating ability over the other two probes. PCR was performed on a gold electrode surface while recording the cathodic peak current by measuring the differential pulse voltammetry (DPV). The peak current was decreases exponentially with an increase in PCR cycle number which was used to derive a calibration plot to quantify the initial copy numbers of the tpc DNA. The detection ability of the described method also verified by gel electrophoresis and circular dichroism methods. The described probes are highly stable under PCR conditions, involve simple preparation protocols and did not inhibit the PCR. Also, the DPV based electrochemical platform offers ultra-sensitivity required for the DNA analysis. The probe AP3 is able to detect low target copies (~103) which is comparable to the detection of real time optical PCR methods and therefore this redox probe has great potential for the development of real time electrochemical PCR monitoring.
論文目次:摘要 i
Abstract ii
誌謝 iv
目錄 v
圖目錄 ix
表目錄 xii
附圖目錄 xiii
第一章 前言 1
第二章 文獻探討 2
2.1 基因 2
2.2 聚合酶鏈鎖反應(Polymerase chain reaction, PCR) 3
2.3 傳統光學基因定量分析方法 5
2.3.1 嵌入型螢光染劑(intercalating dyes) 6
2.3.2 螢光引子(Primer-based chemistries) 6
2.3.3 螢光探針(probe-based chemistries) 7
2.4 電化學分析方法 8
2.4.1 循環伏安法(cyclic voltammetry, CV) 8
2.4.2 微分脈衝伏安法(differential pulse voltammetry, DPV) 11
2.4.3 實驗裝置 12
2.5 電化學基因定量分析方法 12
2.5.1 固相電化學式定量聚合酶鏈鎖反應(solid-phase qPCR) 13
2.5.2 液相電化學式定量聚合酶鏈鎖反應搭配可氧化的鹼基及氧化訊號轉移探針(Solution-phase qPCR with oxidizable base and redox mediator) 14
2.5.3 液相電化學式定量聚合酶鏈鎖反應搭配氧化還原標示探針(Solution-phase qPCR with redox-labeled probe) 16
2.5.4 液相電化學式定量聚合酶鏈鎖反應搭配電化學嵌入型探針(Solution-phase qPCR with intercalating redox reporter) 16
2.5.5 電化學式定量聚合酶鏈鎖反應文獻整理 18
2.6 分子探針設計 20
2.6.1 蒽醌(anthraquinone) 21
2.6.2 聚吡咯(polypyrrole) 22
2.7 圓二色光譜儀(Circular Dichroism, CD) 22
第三章 實驗目的與策略 26
3.1 實驗目的 26
3.2 實驗策略 26
第四章 實驗方法及設備 28
4.1 實驗藥品 28
4.2 實驗儀器 30
4.3 探針合成步驟 31
4.3.1 N,1-dimethyl-N-(2-(N-methyl-9,10-dioxo-9,10-dihydroanthracene-2-carboxamido)ethyl)-1H-pyrrole-2-carboxamide (AP1)合成方法 31
4.3.2 N,1-dimethyl-4-(1-methyl-1H-pyrrole-2-carboxamido)-N-(2-(N-methyl-9,10-dioxo-9,10-dihydroanthracene-2-carboxamido)ethyl)-1H-pyrrole-2-carboxamide (AP2)合成方法 32
4.3.3 N,1-dimethyl-4-(1-methyl-4-(1-methyl-1H-pyrrole-2-carboxamido)-1H-pyrrole-2-carboxamido)-N-(2-(N-methyl-9,10-dioxo-9,10-dihydroanthracene-2-carboxamido)ethyl)-1H-pyrrole-2-carboxamide (AP3)合成方法 33
4.4 DNA樣品配置 34
4.4.1 HTP 質體(plasmid)純化 34
4.4.2 Calf thymus DNA溶液配製 35
4.4.3 DNA定量分析 35
4.5 PCR條件選擇 36
4.6 檢測條件選擇 38
4.7 探針基本性質測定 39
4.7.1 基本電化學性質 39
4.7.2 熱穩定性 40
4.7.3 探針對PCR反應抑制性 41
4.8 探針結合DNA性質檢測 42
4.8.1 圓二色光譜 42
4.8.2 結合常數(Binding constant, Kb) 43
4.8.3 結合位置大小(Binding site size, s) 44
4.8.4 擴散速率(Diffusion coefficient, Df & Db) 44
4.9 定量聚合酶鏈鎖反應終點檢測(End-point qPCR detection) 45
第五章 結果與討論 46
5.1 探針合成 46
5.2 探針基本性質 48
5.2.1 光學性質 48
5.2.2 電化學性質 49
5.3 探針與DNA結合特異性分析 50
5.3.1 循環伏安法測試 50
5.3.2 圓二色光譜測試 51
5.3.3 結合常數(binding constant, Kb) 51
5.3.4 結合位置大小(binding site size, s) 53
5.3.5 擴散速率(diffusion coefficient, D) 53
5.3.6 結合特異性分析探討 54
5.4 電化學定量聚合酶鏈鎖反應 57
5.4.1 聚合酶鏈鎖反應條件選擇 57
5.4.2 探針之熱穩定性 58
5.4.3 探針對於聚合酶鏈鎖反應之抑制性 58
5.4.4 定量聚合酶鏈鎖反應終點檢測 59
第六章 結論 60
參考文獻 61
附錄 71
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