臺灣博碩士論文加值系統

核適體(aptamer)是稀有且有功能性的核酸分子，對於其目標分子(ligand)具有親和性以及專一性。在過去幾年裡，許多高解析結構的aptamer複合物被解析出來，結合的模式與辨識的機制也慢慢被解開。然而，有些核適體複合物的結合行為與機制還不清楚尤其是缺乏結構資訊的分子。在本研究中，我們利用恆溫滴定卡計(ITC)以及圓二色光譜儀(CD)等的分析工具，並且配合上分子模擬的技術來研究DNA 核適體和小分子之間的反應作用機制。

本研究選擇了三個研究系統，第一個選擇的系統是已經有結構資訊的雙股DNA與一小分子藥物(daunomycin)的結合系統，利用此系統來確認我們整合ITC與CD的實驗分析的正確性。實驗結果顯示當溫度上升對反應的自由能更有利；且為反應熵所貢獻。而且，在daunomycin上的amine貢獻了靜電作用力而此促使了反應的進行。另外，在daunomycin-DNA的反應機制中也發現有焓熵補償效應。此研究方法，不僅僅符合了文獻的對此反應機制的推論，還能更深入的討論其反應機制。證明了ITC之熱力研究之合理性與其可能之貢獻。
進一步我們選擇了一個尚未被深入研究討論過而且未知結構的小分子胺基酸(L-Tyrosinamide；L-TyrNH2)以及其核適體之交互作用機制。由熱力學的資訊配合CD圖譜推論此反應行為為一個焓驅動的過程，並且核適體的結構由B-form 轉變為A-form。而這結果也說明了在L-Arm的反應過程也包含有induced-fit的反應機制。L-TyrNH2的amide group和phenolic hydroxyl group在此反應機制中扮演關鍵的角色。另外，值得注意的是Mg2+不僅增強反應的親和力而且幫助改變DNA 核適體的構型。
本研究最後對於核適體的一項值得受到重視的對掌性異構物的辨識做更深入的機制探討。選擇的是對L-argininamide已有少數幾篇研究以及初步的結構資訊，但對於D-form的研究卻完全沒有的DNA 核適體之結合機制的研究。利用我們的研究平台來深入研究DNA 核適體對於對掌性異構物( D和L-argininamide)的辨識機制。由熱力學研究發現L-Arm 和 D-Arm 和核適體的結合都是焓驅動且損失熵的過程，並且在L-Arm的反應過程也包含有induced-fit的反應機制。L-Arm 和 D-Arm 的 amino group的質子化參與靜電作用力且D-Arm與核適體的反應比L-Arm強。由兩異構物熱容量變化的相反趨勢，推測L-Arm 和 D-Arm與核適體結合可能在不同的結合位置而且造成不同構型的結合複合物。為了能夠由分子層面更深入了解核適體和其結合之ligand間的induced-fit的反應機制。我們利用explicit solvent分子動力學模擬(MD)來驗證在aptamer-L-Arm結合時參與的關鍵鹼基和在原子解析下的induced-fit binding過程。結果顯示在反應過程中，由C9與G10先與 L-Arm上的Guanidine作用，隨後A12與反方向的胺基作用，最後C17在和Guanidine作用完成結合程序。結構上aptamer-L-Arm經由一個induced-fit過程而達到一個幾何最佳化。此機制大致可以分成三個特徵階段︰吸附階段、結合反應階段、複合物穩定階段。另外，經由模擬的結果發現D-Arm、L-Arm與核適體的結合位置確實在不同位置，且由氫鍵與靜電作用能量分佈的分析發現D-Arm、L-Arm的反應機制也不太一樣。此結果也符合了實驗上的發現與推論。
本研究利用簡單、方便的研究方式有系統的探討一個DNA-小分子辨識系統。並且提供了aptamer-ligand結合機制的資訊，並且說明了在aptamer-ligand 結合路徑上的細部資訊。此研究的結果可以對於治療藥物的分子設計和分子辨識等分子工程上之應用提供更多的微觀機制資訊，且可結合NMR和X射線結晶學在結構分析的研究上，提供設計核適體辨識系統上的指導方針。

Aptamers are rare functional nucleic acids with binding affinity and specificity to target ligands. In past years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complexes interactions. However, aptamer complex binding behavior and mechanism are not clearly understood especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC), circular dichroism (CD) and molecular dynamics (MD) simulations were useful tools for studying the fundamental binding mechanism between DNA aptamers and small molecules. To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value were carried out.
In this study, we choose three DNA molecules to examine the binding behaviors between these DNA molecules and small ligands. The first system is to illustrate the binding mechanism of daunomycin binding with a simple dsDNA. The results suggest that the binding free energy more favorable with temperature increased; this is contributed by the binding entropy. Furthermore, the amine group on daunomycin contributes electrostatic interaction that induces the binding process. In addition, enthalpy–entropy compensation is also exhibited in the daunomycin–DNA binding mechanism.
Secondly, we examined the binding mechanism between L-Tyrosinamide (L-TyrNH2) and its aptamer. The thermodynamic signature along with the coupled CD spectral change suggests that this binding behavior is an enthalpy driven process. The results showed that the interaction is an induced fit binding. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg2+ not only improves binding affinity but also helps change the structure of DNA aptamer.
The last one is a comparative study of the DNA aptamer binding with L-argininamide (L-Arm) and its enantiomer (D-Arm). The thermodynamics study reveals that both L-Arm and D-Arm binding with the aptamer are an enthalpy driven and entropy cost process, and L-Arm binding with the aptamer involved induced-fit binding mechanism. The protonated amino group of both L-Arm and D-Arm participates in electrostatic interaction and this interaction is stronger for D-Arm than L-Arm binding with the aptamer. From the opposite behavior of the heat capacity change of the two enantiomers, we could suggest that L-Arm and D-Arm bind in different binding site of aptamer and resulted in different conformations of the binding complexes.
From previous studies, we found that induced-fit binding mechanism usually involved in the binding processes between aptamer and ligand. We used explicit solvent MD simulations to examine the critical bases involved in aptamer-L-Arm binding and the induced-fit binding process in atomic resolution. The simulation results revealed that three pairs of bases (C9-C16, G10-C16, and A12-C17) play important roles in aptamer-L-Arm binding and that aptamer-L-Arm binding adopts a geometry optimized through a general induced-fit process. The mechanism has the following characteristic stages: adsorption stage, binding stage and complex stabilization stage.
In addition, simulation results showed that the L-Arm binding location of the aptamer is different with D-Arm. From electrostatic interaction energy profile and hydrogen bonding analysis, the binding mechanisms of D-Arm and L-Arm are also different. These results are in agreement with the experiment inferences. This study used an easy, convenient method of performing a systemic study in recognition systems. This study also provides the information of aptamer-ligand binding mechanism, and shows the detail information of the binding pathway. It provides additional information about microscopic mechanisms useful for molecular design, molecular recognition, and the structural investigation from NMR and X-ray crystallography. This information can offer a guideline for molecular engineering in aptamer recognition design.

摘要 i
Abstract iii
致謝 v
目錄 vii
圖目錄 xi
表目錄 xv
第一章 緒論 1
1.1研究動機 1
1.2研究目的 2
第二章 文獻回顧 5
2.1核酸簡介 5
2.2小分子與核酸作用 6
2.2.1溝槽結合 7
2.2.2崁入結合 8
2.3 RNA World Hypothesis 12
2.4核適體(Aptamer) 13
2.4.1 Systematic Evolution of Ligands by Exponential Enrichments(SELEX) 15
2.4.2核適體(Aptamer)與抗體(Antibody)之比較 17
2.4.3 Riboswitch 23
2.5核適體之相關應用 25
2.5.1 Biosensors與Signaling之應用 25
2.5.2 管柱層析與毛細管電泳之應用 27
2.5.3 藥物發展、治療與臨床之應用 28
2.5.4 奈米科技（nanotechnology）之應用 35
2.5.5 其他生醫上的研究應用 37
2.6 核適體應用上的瓶頸 39
2.7核適體與ligand結合行為 40
2.7.1 結構分析 40
2.7.2 統計實驗與演化分析 42
2.7.3 二級結構預測與序列最小化 43
2.7.4 動力學與熱力學分析 45
2.8分子動態模擬(MD) 48
2.8.1 基本計算原理 49
2.8.2 週期性邊界條件 50
2.8.3 分子力場 51
2.8.4 統計系集(ensemble) 59
第三章 實驗藥品與實驗方法 61
3.1 實驗藥品 61
3.2 儀器設備 62
3.3 實驗方法 62
3.3.1 恆溫滴定卡計 63
3.3.2 圓二色光譜儀 63
第四章 Daunomycin 與DNA的反應機制 65
4.1 摘要 65
4.2 前言 65
4.3 結果與討論 67
4.3.1溫度影響 67
4.3.2 鹽影響 69
4.3.3 pH值 72
4.3.4焓熵補償 74
4.4 結論 76
第五章 L-Tyrosinamide與核適體之反應機制 77
5.1 摘要 77
5.2 前言 77
5.3結果與討論 80
5.3.1 Circular Dichroism 80
5.3.2 溫度效應 82
5.3.3鹽濃度效應 86
5.3.4 pH值的影響與反應質子化過程 89
5.3.5 不同的類似物 92
5.3.6 Mg2+ 影響 93
5.4 結論 95
第六章 Argininamide與核適體之反應機制 97
6.1 摘要 97
6.2 前言 97
6.3結果 99
6.3.1 Circular Dichroism 99
6.3.2 Thermodynamic analysis 101
6.4 討論 109
6.5 結論 110
第七章 Argininamide與核適體反應機制之分子動態模擬 111
7.1 摘要 111
7.2 前言 111
7.3 實驗方法與分析 113
7.3.1 模擬系統 113
7.3.2 計算 114
7.3.3 座標分析 114
7.4 結果與討論 115
7.4.1 Arm-Aptamer Complex的平衡模擬 115
7.4.2 Arm-Free aptamer的平衡模擬 117
7.4.3 Induced-fit模擬結構分析 119
7.4.4 Induced-fit驅動力 125
7.4.5 D-, L-Argininamide form模擬比較分析 129
7.5 結論 135
第八章 總結 137
第九章 未來研究方向 139
第十章 References 141
第十一章 附錄 165

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