臺灣博碩士論文加值系統

前列腺癌近幾年在全球男性癌症發生率及癌症死亡率中比率相當高，臨床上最常用前列腺特異性抗原 (prostate-specific antigen, PSA) 來檢測，其檢測的缺點是專一性有限導致診斷率失準。miRNA是內源性非編碼RNA，它們會透過與特定的mRNA結合並抑制蛋白轉譯影響基因表現，因此偵測miRNA的表現量異常對於臨床醫療的早期診斷是相當重要的。至今有許多研究致力於開發檢測miRNA的方法，但是在應用上面臨到許多的限制，包括專業儀器與專業技術人員的操作及成本考量等，因此miRNA的偵測方法仍有許多發展的空間。
在先前研究中發現前列腺癌患者的microRNA-141 (miR-141) 相對於健康受試者過度表現。本研究欲開發以偵測前列腺癌生物標記物miR-141之DNA水凝膠微膠囊；利用包裏Tetramethylrhodamine-modified dextran (TMR-D) /量子點 (quantum dots, QDs) 的碳酸鈣球為模板，在表面修飾具有啟動子功能的核酸，接著加入髮夾型核酸修飾的聚丙烯醯胺，啟動子會觸發核酸雜交鏈鎖反應 (hybridization chain reaction, HCR) ，藉核酸雜交將丙烯醯胺高分子固定至碳酸鈣球表面形成水凝膠殼層，待碳酸鈣球模板溶解後形成包裹螢光訊號的DNA水凝膠微膠囊。微膠囊殼層中嵌有miR-141的互補序列，當環境中存在miR-141便會與微膠囊中的互補序列產生序列置換反應 (strand displacement reaction) 使微膠囊瓦解並釋放螢光，利用釋放之螢光對miR-141進行定量分析。為使微膠囊的偵測靈敏度提高，本研究結合酵素協助序列置換放大法，將miR-141 與設計之髮夾型核酸序列、輔助序列及酵素進行反應，以產出大量miR-141相似物，再以DNA水凝膠微膠囊進行偵測。
本研究已成功合成出載有TMR-D/量子點的DNA水凝膠微膠囊，並對於miR-141具有選擇性，且可隨時間及miR-141的濃度有相對應的量子點釋放，且可藉由酵素協助序列置換放大法增加DNA水凝膠微膠囊偵測miR-141的靈敏度，在經過放大系統之後，DNA水凝膠微膠囊的偵測極限為44.9 pM，且在10 % FBS的基質效應測試可有效放大miR-141並使微膠囊釋放相對的螢光量子點。

Prostate cancer is quite high in male cancer incidence and mortality in the worldwide. Currently, prostate-specific antigen (PSA) is the most commonly used to detect prostate cancer. The fault of its detection method is limited specificity leading to diagnostic error. miRNAs are endogenous, non-coding RNAs that affect gene expression by binding to specific mRNAs and inhibiting protein translation. Therefore, detecting abnormal expression of miRNAs is important for early diagnosis of clinical care. Many studies have been devoted to the development of methods for detecting miRNAs, but there are many limitations at the application level, including the professional instruments and professional technicians and cost. So, there are still many barriers for miRNA detection methods.
In previous studies, it was found that miR-141 in prostate cancer patients was overexpressed. This study develop a DNA hydrogel microcapsule for detect prostate cancer biomarker miR-141; using a calcium carbonate particles with Tetramethylrhodamine-modified dextran (TMR-D)/quantum dots (QDs) as templates modified with nucleic acid sequences as promoter on the surface, and then adding the hairpin-type nucleic acid-modified acrylamide polymer, the promoter on the particle surface triggers nucleic acid to start hybridization chain reaction (HCR), and the acrylamide polymer is immobilized on the surface of the calcium carbonate sphere from the hydrogel shell layer. After the calcium carbonate particles are dissolved, DNA hydrogel microcapsules encapsulating TMR-D/QDs were formed. The complementary sequence of miR-141 is embedded in the microcapsule shell. When miR-141 is present in the environment, miR-141 will cause a strand displacement reaction with the complementary sequence in the microcapsules, causing the microcapsules to collapse and release the fluorescence signal. The quantitative analysis of miR-141 can be performed using the fluorescence intensity of the release. In order to improve the detection sensitivity of microcapsules, this study combined with enzyme-assisted sequence displacement amplification. miR-141 react with specially designed amplifier-hairpin, auxiliary strand and enzymes generate a large number of miR-141 analogs before DNA hydrogel microcapsules detection.
In this study, DNA hydrogel microcapsules loaded with TMR-D/quantum dots have been successfully synthesized and they have specific selectivity for miR-141, and have corresponding quantum dots release with time and concentration of miR-141.
The sensitivity of the DNA hydrogel microcapsules to detect miR-141 can be increased by enzyme-assisted sequence displacement amplification. After the amplification system, the limit of detection is 44.9 pM. The microcapsules can effectively release relative fluorescence intensity by amplified miR-141 at 10% FBS.

目錄
致謝 I
中文摘要 II
英文摘要 III
目錄 IV
圖目錄 VII
表目錄 IX
一、 前言 1
1.1 研究動機 1
1.2 前列腺癌的生物標記物 (biomarker) 2
1.3 miR-141 4
1.4 偵測miRNA之方法 5
二、 實驗材料與方法 7
2.1 藥品試劑 7
2.2 實驗儀器 10
三、 階段一：設計、合成及鑑定DNA水凝膠微膠囊 11
3.1 前言 11
3.1.1 去氧核醣核酸 (deoxyribonucleic acid, DNA) 水凝膠 (hydrogel) 微膠囊 11
3.1.2 雜交鏈鎖反應 (Hybridization Chain Reaction, HCR) 12
3.1.3 DNA水凝膠微膠囊設計構想 13
3.2 實驗材料與方法 15
3.2.1 去氧核醣核酸 (DNA) 序列 15
3.2.2 合成DNA 共軛聚合物 15
3.2.2 合成聚丙烯酸 (poly (acrylic acid), PAA) 修飾的promoter 16
3.2.3 量子點移相 16
3.2.4 合成包裹Tetramethylrhodamine-modified dextran (TMR-D) /量子點 (Quantum dot, QD) 碳酸鈣顆粒 16
3.2.5 合成DNA水凝膠修飾碳酸鈣顆粒 17
3.2.6 形成DNA水凝膠微膠囊 17
3.2.7 共軛焦雷射螢光顯微鏡 (Confocal Laser Fluorescence Microscope, CLFM/CLSM) 鑑定DNA水凝膠微膠囊 18
3.2.8 掃瞄式電子顯微鏡 (Scanning Electron Microscope, SEM) 鑑定DNA水凝膠微膠囊 18
3.2.9 能量散佈分析儀 (Energy Dispersive Spectrometer, EDS) 鑑定DNA水凝膠微膠囊 19
3.2.10 丙烯醯胺與丙烯酸基團修飾的核酸分子結合比例的測定 19
3.3 實驗結果與討論 20
3.3.1 DNA水凝膠微膠囊的鑑定-共軛焦雷射螢光顯微鏡 20
3.3.1.1 鑑定裝載TMR-D的DNA水凝膠微膠囊 20
3.2.1.2 鑑定裝載QDs的DNA水凝膠微膠囊 23
3.3.2 DNA水凝膠微膠囊的鑑定-掃瞄式電子顯微鏡 29
3.3.3 DNA水凝膠微膠囊的鑑定-能量散佈分析儀 30
3.3.4 丙烯醯胺與丙烯酸基團修飾的核酸分子結合比例的測定 31
3.4 結論 32
四、階段二：核酸觸發微膠囊釋放測試 33
4.1 前言 33
4.1.1 序列置換反應 (Strand Displacement Reaction, SDR) 33
4.1.2 微膠囊釋放機制 34
4.2 實驗材料與方法 35
4.2.1 去氧核醣核酸 (DNA) 序列 35
4.2.2 序列選擇性測試 35
4.2.3 不同作用時間對於釋放之測試 35
4.2.4 不同miR-141濃度對於微膠囊釋放之測試 35
4.2.5 螢光光譜儀測試微膠囊釋放之螢光強度 36
4.2.6 基質效應測試 36
4.3 實驗結果與討論 37
4.3.1 裝載TMR-D DNA水凝膠微膠囊釋放測試 37
4.3.2 裝載QDs DNA水凝膠微膠囊合成條件最佳化 38
4.3.3 裝載QDs DNA水凝膠微膠囊釋放測試 40
4.3.3.1 序列選擇性測試 40
4.3.3.2 不同作用時間對於釋放之測試 41
4.3.3.3 不同miR-141濃度對於微膠囊釋放之測試 42
4.3.4 基質效應測試 43
4.3.5 微膠囊一致性測試 44
4.3.4.1 同批合成不同天測試 (day to day) 44
4.3.4.2 不同批同條件測試 (batch to batch) 45
4.4 結論 46
五、階段三：目標偵測物訊號放大策略 48
5.1 前言 48
方法一： 置換序列放大反應 48
5.2 實驗材料與方法 49
5.2.1 去氧核醣核酸 (DNA) 序列 49
5.2.2 序列置換作用效率之測試 49
5.3 實驗結果與討論 50
5.4 結論 51
方法二： 酵素協助序列置換放大法 52
5.5 實驗材料與方法 54
5.5.1 去氧核醣核酸 (DNA) 序列 54
5.5.2 序列雜交測試 54
5.5.3 酵素協助序列置換放大測試 54
5.5.4 酵素協助序列置換放大結合DNA水凝膠微膠囊 55
5.5.5 基質效應測試 55
5.6 實驗結果與討論 56
5.6.1 序列雜交測試 56
5.6.2 Auxiliary Strand (AS) 與New Auxiliary Strand (NAS) 放大效率測試 58
5.6.3 Auxiliary Strand Hairpin (ASHP) 放大效率測試 59
5.6.3.1 酵素比例放大效率測試 59
5.6.3.2 反應時間放大效率測試 61
5.6.3.3 酵素濃度最佳化放大測試 63
5.6.3.4 不同濃度miR-141放大測試 65
5.6.4 酵素協助序列置換放大法結合DNA水凝膠微膠囊 66
5.6.5 基質效應測試 67
5.7 結論 68
六、 結論與未來展望 69
七、 參考文獻 71
附錄一 去氧核醣核酸 (DNA) 序列 77 
圖目錄
圖 1 miR-141在前列腺癌細胞中的調節途徑。 4
圖 2 雜交鏈鎖反應 (HCR) 示意圖。 12
圖 3 DNA水凝膠微膠囊結構及合成示意圖。 14
圖 4 共軛焦雷射螢光顯微鏡 (CLSM) 觀察裝載TMR-D碳酸鈣顆粒的影像。 21
圖 5 共軛焦雷射螢光顯微鏡 (CLSM) 觀察DNA水凝膠修飾裝載TMR-D碳酸鈣顆粒的影像。 22
圖 6 共軛焦雷射螢光顯微鏡 (CLSM) 觀察裝載QDs的碳酸鈣顆粒的影像。 25
圖 7 共軛焦雷射螢光顯微鏡觀察 poly (acrylamine hydrochloride) (PAH) 修飾裝載QDs的碳酸鈣顆粒的影像。 26
圖 8 共軛焦雷射螢光顯微鏡觀察PAH及poly (acrylic acid) (PAA)-promoter修飾的裝載QDs的碳酸鈣顆粒的影像： 27
圖 9 共軛焦雷射螢光顯微鏡觀察DNA水凝膠修飾裝載QDs的碳酸鈣顆粒及DNA水凝膠微膠囊的影像。 28
圖 10 利用SEM觀察 (A) 包裹QDs的碳酸鈣顆粒、 (B) 修飾DNA水凝膠修包裹QDs的碳酸鈣顆粒及 (C) 裝載QDs的DNA水凝膠微膠囊。 29
圖 11 (A)包裹QDs碳酸鈣顆粒的SEM影像，圈選處為EDS偵測位置； (B) EDS分析結果； (C) DNA水凝膠修飾的包裹QDs碳酸鈣顆粒的SEM影像，圈選處為EDS偵測位置； (D) EDS分析結果。 30
圖 12 H1共軛聚合物上核酸單元和丙烯醯胺單體單元之間的比例。 31
圖 13 H2H共軛聚合物上核酸單元和丙烯醯胺單體單元之間的比例。 31
圖 14 序列置換反應 (SDR) 示意圖。 33
圖 15 微膠囊釋放螢光訊號機制示意圖。 34
圖 16 裝載TMR-D DNA水凝膠微膠囊不同濃度miR-DNA的釋放結果。 37
圖 17 合成裝載QDs DNA水凝膠微膠囊條件最佳化。 39
圖 18 微膠囊序列專一選擇性測試結果。 40
圖 19 相同濃度的miR-141與微膠囊不同作用時間的測試。 41
圖 20 不同miR-141濃度對於微膠囊釋放之測試。 42
圖 21 基質效應測試。 43
圖 22 同批合成不同天測試結果 (day to day)。 44
圖 23 不同批微膠囊相同條件測試結果 (batch to batch)。 45
圖 24 置換序列和miR-141在微膠囊中作用示意圖。 48
圖 25 不同作用條件測試序列置換的最佳條件。 50
圖 26 酵素協助序列置換放大反應過程及產物與微膠囊作用之示意圖。 53
圖 27 Nt.BbvcI及Bst DNA polymerase 作用機制示意圖。 53
圖 28 序列雜交測試。 57
圖 29 使用miR-141、Amplifier-Hairpin (HP) 、Auxiliary Strand (AS) /New Auxiliary Strand (NAS) 測試酵素協助序列置換放大的結果。 58
圖 30 酵素比例放大測試結果。 60
圖 31 反應時間放大效率測試結果。 62
圖 32 酵素濃度放大效率測試結果。 63
圖 33 酵素濃度放大效率測試結果。 64
圖 34 不同濃度miR-141放大測試結果。 65
圖 35 酵素協助序列置換放大法結合DNA水凝膠微膠囊釋放之測試。 66
圖 36 基質效應測試。 67

 
表目錄
表 1 DNA水凝膠微膠囊之相關核酸序列 15
表 2 序列選擇性實驗相關序列。 35
表 3 置換序列放大反應相關序列。 49
表 4 酵素協助序列置換放大法相關序列。 54
表 5 miRNA偵測系統之文獻比較 70
表 6 DNA水凝膠微膠囊及放大策略之相關核酸序列 77

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