本篇論文內容以發展新型生物感測方法及合成奈米粒子應用於感測器，開發高靈敏及選擇性之偵測技術，用於偵測生物小分子、金屬離子及酵素活性。研究內容分為四個部分：
（一）以腺苷高半胱胺酸酶活性抑制法偵測腺苷及磷酸酶活性：
以腺苷 (adenosine) 抑制腺苷高半胱胺酸水解酶 (S-adenosylhomocysteine hydrolase, SAHH)，使SAHH催化水解腺苷高半胱胺酸 (S-adenosylhomocysteine, SAH) 反應速率減慢，導致SAH水解產物同半胱胺酸(homocysteine, HCys) 減少，水解產物HCys與溶液中adenosine量成反比，其中HCys與衍生試劑2,3-naphthalenedicarboxaldehyde (NDA) 反應形成有螢光之產物，以NDA衍生水解產物偵測腺苷濃度，依螢光值減少程度對腺苷進行定量，以adenosine抑制SAHH酵素活性為基礎設計的方法，偵測adenosine之偵測極限為0.3 μM，區分adenosine及其類似物的選擇性可達100倍，並且可應用於偵測尿液樣品中adenosine含量，又因SAHH酵素對adenosine及單磷酸腺苷(adenosine monophosphate, AMP) 抑制反應速率不同，以單磷酸腺苷為鹼性磷酸酶受質，AMP水解後產生adenosine，接著以抑制SAHH酵素活性之螢光偵測方法，應用此研究方法於鹼性磷酸酶活性偵測。
（二）利用非華森-克里克之分子信籤設計雙輸入及三輸入分子邏輯閘：
利用一條DNA分子信籤探針，序列兩端分別修飾螢光團及消光基團，因鹼基與金屬離子或小分子之間有非華森-克里克作用力，鹼基thymine、cytosine及adenine分別與Hg2+、Ag+及coralyne結合，各別形成T-Hg2+-T、C-Ag+-C及A2-coralyne-A2結構，這些金屬離子或分子加入使分子信籤探針構形改變，序列末端螢光團及消光團靠近發生碰撞消光現象而使螢光消光，再者移除Hg2+、Ag+及coralyne這三種物質可各別加入含硫分子、碘離子與氰化物、polyadenosine等物質，致使分子信籤探針結構改變、螢光團與消光團遠離而螢光回復，利用這些離子及分子與DNA之間作用力，以這些離子或分子作為邏輯匣化學刺激的輸入來源，分子信籤探針螢光強度產生變化作為輸出，以此為基礎使用單一條DNA序列設計雙輸入 (OR, AND, INHIBIT,NOR, NAND及REVERSE IMPLICATION)與三輸入 (OR, NOR及AND) 分子邏輯閘，並且達成可逆邏輯操作。
（三）金奈米粒子聚集之雷射誘導瑞利散射偵測鉀離子、鉛離子及酵素活性：
金奈米粒子聚集時散射光會大幅增加，研究中以金奈米粒子作為光散射感測器，使用532 nm雷射探討光散射的性質與金奈米粒子聚集偵測目標分析物，利用粒子聚集之雷射誘導瑞利散射偵測鉀離子、酵素活性及鉛離子，實驗中討論使用金奈米粒子粒徑尺寸大小對分散及聚集情況產生散射光增益之影響，並且選用鉀離子適合體吸附之金奈米粒子、氟界面活性劑修飾之金奈米粒子、修飾gallic acid的金奈米粒子，針對三種不同的分析物－鉀離子、SAHH及鉛離子，分別進行目標物誘導聚集之散射光偵測，由聚集之金奈米粒子光散射程度較分散之金奈米粒子強對分析物定量，此方法與一般比色法偵測分析物靈敏度改善最少10倍，並且裝置可透過雷射筆及智慧型手機達成微型化偵測之目的。
（四）氫氧自由基裂解聚多巴胺合成螢光奈米粒子及感測器應用：
利用鹼性下合成的聚多巴胺奈米粒子，以由上而下方式使用氫氧自由基降解聚多巴胺奈米粒子，將粒子由大粒徑轉為小粒徑具有螢光之奈米粒子，首先以穿透式顯微鏡、暗視野顯微鏡、熱重分析、傅里葉轉換紅外光譜、雷射脫附質譜等方法，對螢光多巴胺奈米粒子鑑定分析，並且螢光聚多巴胺奈米粒子光學吸收與放光光學行為與真黑色素類似，具有寬廣吸收譜帶及放光光譜隨激發波長改變位移，計算螢光量子產率為1.2%，隨後應用合成的螢光聚多巴胺奈米粒子富有鄰苯二酚結構之特性，以catechol官能基與鐵離子形成配位，光源激發粒子後，激發態電子氧化轉移至鐵離子，兩者之間產生光誘導電子轉移，使螢光聚多巴胺粒子放光消光，以此對鐵離子定量分析，偵測極限為0.3 μM。

The purpose of this thesis is to describe how to develop molecular- and nanomaterial-based biosensor for sensing biomolecules and metal ions. The thesis consists of four independent works. (1) A simple and label-free fluorescent method for sensitive and selective detection of adenosine in urine sample was developed based on adenosine-induced inhibition of adenosylhomocysteine hydrolase (SAHH) activity. Without the addition of nucleophile, 2,3-naphthalenedicarboxaldehyde (NDA) was found to selectively react with homocysteine to form fluorescent product. Adenosine is efficient to inhibit the production of homocysteine from the hydrolysis reaction between SAHH and adenosylhomocysteine. Taken together, the fluorescence of NDA-homocysteine derivatives decreased with an increase in the adenosine concentration. As a result, the SAHH-based probe provided high sensitivity (a limit of detection for adenosine of 0.3 μM) and high selectivity (more than 100-fold for andenosine over any adenosine analogs). (2) A set of two-input and three-input DNA logic gates was constructed using non-Waston-Crick base pairing-based molecular beacon (MB). The presence of Hg2+, Ag+, and coralyne promoted the conformational changes of MB via the formation of T-Hg2+-T, C-Ag+-C, and A2-coralyne-A2 coordination, resulting in its fluorescent quenching. It was found that thiols, complexing agents, and polyadenosine can remove Hg2+, Ag+, and coralyne from the hairpin-shaped MB, respectively. Based on these phenomenon, the designed MB generated a series of two-input, three-input, and set-reset logic operation at the molecular level. (3) Laser-induced light scattering technique with the adevantages of high sensitivity, low cost, portability, and miniaturization was applied for sensing three gold nanoparticle-based sensing systems, including salt-, thiol-, and metal ion-induced nanoparticle aggregation. The combination of a miniatuarized spectrometer with a 532-nm laser allows the sensitive detection of Rayleigh scattering from nanoparticles aggregation. As a result, the proposed system provided more than 10-fold sensitivity improvement as compared to colorimetric assay. (4) Fluorescent polydopamine particles was prepared through hydroxyl-radical degradation of polydopamine nanoparticles. The production of fluorescent polydopamine was demonstrated using transmission electron microscope, dark field microscope, and thermogravimetric analyzer. The possible chemical compositions of polydopamine dots were determined using Fourier transform infrared spectrosmeter and laser desorption/ionization-time-of-flight mass spectrometer. Additionally, fluorescent polydopamine dots were used for sensitive and selective detection of Fe(III) through coordination between the catechol group of fluorescent polydopamine dots and Fe(III). This sensing mechanism relied on electron-transfer-induced fluorescence quenching.

論文審定書.................................................................................................................i
摘要…………………………………………………………………………………ii
目錄…………………………………………………………………………………vi
圖目錄……………………………………………………………………………xii
表目錄……………………………………………………………………………xv
縮寫表……………………………………………………………………………xvi

第壹章　緒論………………………………………………………………………1
1.1 分子螢光感測器………………………………………………………1
1.1.1 螢光感測器機制………………………………………………..1
1.1.1.1 光誘導電子轉移………………………………………1
1.1.1.2 分子內電荷轉移………………………………………2
1.1.1.3 螢光共振能量轉移……………………………………2
1.1.1.4 激發態二聚體…………………………………………2
1.1.1.5 聚集誘導發光…………………………………………3
1.1.2 有機分子螢光感測器之應用…………………………………3
1.2 DNA感測器…………………………………………………………5
1.2.1 DNA構形及鍵結形式…………………………………………5
1.2.1.1 Watson-Crick base pairs………………………………5
1.2.1.2 non-Watson-Crick base pairs…………………………5
1.2.1.2.1 髮夾結構…………………………………..5
1.2.1.2.2 三股DNA………………………………….6
1.2.1.2.3 G-quadruplex………………………………6
1.2.1.2.4 i-motif……………………………………6
1.2.1.2.5 DNA與金屬離子或小分子之結合體……6
1.2.2 以DNA為基礎之感測器………………………………………8
1.2.2.1 適合體…………………………………………………8
1.2.2.2 具催化活性之DNA感測器…………………………10
1.2.2.3 分子信籤感測器……………………………………..11
1.2.2.4 DNA放大技術……………………………………….13
1.2.2.4.1 DNA雜合鏈鎖反應……………………...13
1.2.2.4.2 滾環循環擴增技術………………………14
1.3 金奈米粒子感測器…………………………………………………..15
1.3.1 合成及修飾金奈米粒子………………………………………15
1.3.1.1 合成金奈米粒子方法……………………………..…15
1.3.1.2 修飾金奈米粒子方法………………………………..16
1.3.2 金奈米粒子光學性質及催化活性……………………………17
1.3.2.1 定域化表面電漿共振………………………………..17
1.3.2.2 螢光消光……………………………………………..18
1.3.2.3 催化特性……………………………………………..18
1.3.3 金奈米粒子感測器……………………………………………18
1.3.3.1 比色法………………………………………………..18
1.3.3.2 螢光法………………………………………………..19
1.3.3.3 電化學方法…………………………………………..20
1.3.3.4 散射法………………………………………………..20
1.3.3.5 表面增強拉曼散射法………………………………..22
1.4 聚多巴胺……………………………………………………………..23
1.4.1 聚多巴胺聚合機制……………………………………………23
1.4.2 聚多巴胺之性質………………………………………………23
1.4.2.1 化學反應性…………………………………………..23
1.4.2.2 電學性質……………………………………………..24
1.4.2.3 光學性質……………………………………………..24
1.4.3 聚多巴胺感測器………………………………………………25
1.4.3.1 電化學感測器……………………….………………25
1.4.3.2 比色感測器…………………………………………..26
1.4.3.3 螢光感測器…………………………………………..26
1.5 分子邏輯匣…………………………………………………………..27
1.5.1 分子邏輯匣基本概念…………………………………………27
1.5.2 單輸入與雙輸入邏輯匣………………………………………27
1.5.3 驅動分子邏輯匣及轉換訊號…………………………………29
1.5.3.1 化學驅動分子邏輯匣………………………………..29
1.5.3.2 光驅動邏輯匣………………………………………..30
1.5.3.3 電化學驅動分子邏輯匣及磁性轉換………………..30
1.5.4 生物分子系統之分子邏輯匣…………………………………31
1.5.4.1 核酸分子邏輯匣……………………………………..31
1.5.4.2 蛋白質分子邏輯匣…………………………………..32
1.6 研究動機……………………………………………………………..33
1.7 參考文獻……………………………………………………………..35

第貳章　以腺苷高半胱胺酸酶活性抑制法偵測腺苷及磷酸酶活性...45
2.1 摘要…………………………………………………………………..45
2.2 前言…………………………………………………………………..45
2.3 實驗部分……………………………………………………………..49
2.3.1 實驗藥品………………………………………………………49
2.3.2 樣品製備方法…………………………………………………49
2.3.3 儀器設備………………………………………………………50
2.4 結果與討論…………………………………………………………..51
2.4.1 偵測原理………………………………………………………51
2.4.2 證明NDA-HCys衍生物生成…………………………………53
2.4.3 偵測溶液中腺苷濃度…………………………………………60
2.4.4 偵測鹼性磷酸酶活性…………………………………………66
2.5 結論…………………………………………………………………..70
2.6 參考文獻……………………………………………………………..71

第參章　利用非華森-克里克之分子信籤設計雙輸入及三輸入分子邏輯閘..........................................................................................................77
3.1 摘要…………………………………………………………………..77
3.2 前言…………………………………………………………………..77
3.3 實驗部分……………………………………………………………..80
3.3.1 實驗藥品………………………………………………………80
3.3.2 樣品製備方法…………………………………………………80
3.3.3 儀器設備………………………………………………………82
3.4 結果與討論…………………………………………………………..83
3.4.1 分子信籤探針性質與定量……………………………………83
3.4.2 雙輸入分子邏輯匣……………………………………………94
3.4.3 三輸入分子邏輯匣及可逆操作………………………………99
3.5 結論…………………………………………………………………102
3.6 參考文獻……………………………………………………………103
第肆章　金奈米粒子聚集之雷射誘導瑞利散射偵測鉀離子、鉛離子及酵素活性...............................................................................................115
4.1 摘要…………………………………………………………………115
4.2 前言………………………..………………………………………..115
4.3 實驗部分……………………………………………………………119
4.3.1 實驗藥品……………………………………………………..119
4.3.2 樣品製備方法………………………………………………..119
4.3.3 儀器設備……………………………………………………..120
4.4 結果與討論…………………………………………………………122
4.4.1 鹽類導致金奈米粒子聚集偵測鉀離子……………………..122
4.4.2 HCys導致金奈米粒子聚集偵測SAHH活性………………128
4.4.3 金奈米粒子交聯聚集偵測鉛離子…………………………..133
4.4.4 利用智慧型手機作為重金屬離子讀取工具………………..134
4.5 結論…………………………………………………………………138
4.6 參考文獻……………………………………………………………139

第伍章　氫氧自由基裂解聚多巴胺合成螢光奈米粒子及感測器應用.............................................................................................................147
5.1 摘要…………………………………………………………………147
5.2 前言…………………………………………………………………147
5.3 實驗部分……………………………………………………………150
5.3.1 實驗藥品……………………………………………………..150
5.3.2 樣品製備方法………………………………………………..150
5.3.3 儀器設備……………………………………………………..151
5.4 結果與討論…………………………………………………………155
5.4.1 鑑定氫氧自由基裂解之聚多巴胺奈米粒子………………..155
5.4.2 螢光聚多巴胺粒子光學性質及穩定性……………………..160
5.4.3 螢光聚多巴胺粒子光學感測器之應用……………………..167
5.5 結論…………………………………………………………………171
5.6 參考文獻……………………………………………………………172

第陸章　總結論………………………………………………………………...182
附錄…………………………………………………………………………………185

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