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研究生: 吳 坦
Patil, Uttam
論文名稱: 設計與建構互補單鏈去氧核醣核酸之「功能化奈米碳管」暨 發展羅氏光裂解酮酸酯之新反應
Design and Study of Functionalized Carbon Nanotubes as Complimentary Strand of ssDNA and Norrish Type Photo-degradation of β-Ketoester
指導教授: 胡紀如
Hwu, Jih-Ru
口試委員: 彭之皓
Peng, Chi-How
王聖凱
Wang, Sheng-Kai
謝發坤
SHIEH, FA-KUEN
許銘華
Hsu, Ming-Hua
蔡淑貞
Tsay, Shwu-Chen
學位類別: 博士
Doctor
系所名稱: 理學院 - 化學系
Department of Chemistry
論文出版年: 2020
畢業學年度: 108
語文別: 英文
論文頁數: 118
中文關鍵詞: 光降解單層壁奈米碳管去氧核糖核酸纏繞酮酸酯光降解
外文關鍵詞: SWCNT, SWCNT, DNA entwinement, ketoesters, photodegradation
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  • 隨著奈米技術之進步,應用於人類疾病之奈米醫學領域隨之蓬勃發展。近十年來,奈米碳管(CNTs)及其支架,已被應用於數個領域,如材料科學,生物傳感,成像,紡織工業,藥物輸送,及診斷應用。小尺寸,強度,以及顯著物理特性,使奈米碳管成為一種非常獨特的材料。如何減少單壁奈米碳管(SWCNTs)於人體中之毒性一直被廣為研究。本篇論文中利用表面改性以減輕單壁奈米碳管的毒性,並同時賦與其生物辨識功能。雖然SWCNTs曾被用於傳遞單鏈DNA (ssDNA),其能經由非共價結合與ssDNA相互作用。但根據文獻,SWCNTs欲與ssDNA連結目前還是一門困難的技術。
    本論文中首次利用“醫療之神所持蛇杖”的概念設計ssDNA修飾之SWCNT,其中SWCNT似“杖”,而單鏈DNA(ssDNA)像“蛇”。利用核鹼基官能化後之SWCNT做為DNA單鏈,可模擬DNA雙螺旋之共軛互補性質。 本實驗室設計並合成了四個(聚dN)-SWCNT(N = A,T,G和C)。 這些SWCNT經由纏繞ssDNA形成“擬DNA雙股螺旋”。其上之ssDNA可以藉由調整溫度或pH值,以可控方式脫離SWCNT。
    本論文中所研究之另一種藥物載體材料,為由α-酮酸酯構成,可光降解之聚乳酸-共-乙醇酸(PLGA)共聚物。 PLGA是一類可生物降解和生物相容的聚合物,具極高物理強度,已被廣泛研究並做為藥物、蛋白質、及大分子(如DNA,RNA和肽)之傳遞載體。
    聚合物材料現今常被用於可控藥物輸送技術,其易於改造並做工業化大規模生產。 在過去二十年,PLGA被頻繁應用為藥物載體。 PLGA具廣區間之侵蝕時間,易於調整其性質,已被美國食品藥品監督管理局批准用於人體。我們發明一種嶄新方法以合成骨架中包含(甲基)矽烷單元之β-酮酸酯,並成功地以67-81%的效率獲得產物。 該等β-酮酸酯為可光降解PLGA之單體單元。一系列含矽的β-酮酸酯已由酯基團α位進行C-烷基化反應得到。 所得之β-酮酸酯在用紫外線光輻照後,成功經由矽定向Norrish型光裂解反應降解成小片段。
    本論文討論並解決了兩個主題。 首先是可用於ssDNA的傳遞之核鹼基官能化納米碳管(聚dN)SWCNT(N = A,C,G和T)。 ssDNA @(poly dN)-SWCNTs之物理、化學、及生化特性與雙螺旋DNA相似。 其可利用SWCNTs為載體,精準傳遞ssDNA至細胞中。 另一方面,我們並研究了“矽基酮酸酯”之“諾氏光降解反應”。 這種新方法可以用於有機矽化合物以及含矽光降解聚合物之合成,未來可應用做為光控藥物載體材料。


    Nanomedicine are rapidly developing science where nanoscale materials are engaged to serve as means to deliver therapeutic agents to specific targeted sites in a controlled manner. Carbon nanotubes (CNTs) have been explored over past three decades as handy nanoscaffolds for applications in various fields such as material science, biosensing, imaging, textile industry, drug delivery and diagnostic applications. Their small dimensions, strength and the significant physical properties mark them as a very unique material. Expanded use of single-walled carbon nanotubes SWNTs in living systems requires strategies to diminish their cytotoxicity. Modifications of the surface so that mitigate the toxicity of SWNTs and simultaneously enabling specific biological recognition are highly pursued topics for research. SWCNTs have been used to deliver ssDNA as they tend to interact with ssDNA through non-covalent binding. However, reports suggest that ssDNA are difficult to bind carbon nanotubes with low transferring efficiency to cells.
    Herein, this report is the first to link the concept of Rod of Asclepius to the complementary nature of double-stranded DNA wherein SWCNT resembles the “rod” and single-stranded DNA (ssDNA) as the “serpent”. The complementary nature of DNA double helix was emulated by replacement of one DNA strand with nucleobase-functionalized SWCNTs. Our laboratory designed and synthesized four (poly dN)-SWCNTs (N = A, T, G, and C) as a set of biochemical rods. Each of these SWCNTs performed like a complementary strand and formed a “pseudo-double helix” with ssDNA by entwinement. This pseudo form aided the ssDNA to dissociate from the rods in a controlled manner when affected by temperature and pH value.
    After successfully achieved the pseudo double helical structure, I focused on to photodegrade -ketoesters that are co-polymers for poly lactic-co-glycolic acid (PLGA). PLGA are a class of biodegradable and biocompatible polymers, which are physically strong and have been comprehensively studied as delivery vehicles for drugs, proteins, and macromolecules such as DNA, RNA, and peptides.
    Polymers are another class of materials widely used in controlled drug delivery technology owing to their easy production at industrial scale and potential for additional alteration in a synchronized manner. Over past two decades, PLGA has attracted attention as polymeric candidate for fabrication of devices for drug delivery and tissue engineering applications. PLGA displays a wide range of erosion time, its mechanical properties can be easily tuned and most notably it is a FDA approved polymer.
    I designed a new method to synthesize β-ketoesters containing (methyl)silane units in the skeleton and successfully obtained them in 67–81% yields. These β-ketoesters are monomer units to obtain photodegradable PLGA. I have synthesized a series of silicon-containing β-ketoesters by C-alkylation at the α-position of the ester group. These β-ketoesters degraded into fragments after photo-irradiation with UV light, suggesting the degradation followed silicon-directed Norrish type photo-cleavage.
    Two major issues has been discussed and solved in this dissertation. The nucleobase-functionalized nanotubes (poly dN)SWCNTs (N = A, C, G and T) were utilized for the delivery of ssDNA. ssDNA@(poly dN)-SWCNTs exhibit similar physical, chemical and biochemical properties to those of the double helical DNA. Their properties deviate from and are even superior to those of DNA-entwined pristine SWCNTs. These findings pave a way to enable ssDNA delivered to the targets in the cells with SWCNTs as a vehicle. On the other hand we have studied the “Norrish Type photo-degradation” of “silicon directed ketoesters”. This new method can serve as reference material for the future synthesis of organosilicon compounds and silicon-containing photodegradable polymers.

    Abstract (in English) ………………………………………………………………...i Abstract (in Chinese) ……………………………………………………………….iv Acknowledgement …………………………………………………………………..vi Content ……………………………………………………………………………..viii List of Figures ………………………………………………………………….......xiv List of Tables ……………………………………………………………………......xv List of Schemes …………………………………………………………………….xvi 1. Introduction ……………………………………………………………………..1 2. Results ………………………………………………………………………….29 2.1 Synthesis of nucleobase-functionalized single-walled carbon nanotubes (poly dN)-SWCNTs (N = A, T, G and C) 1...…………………………………............29 2.2 Hybridization of ssDNA 2 with (poly dN)-SWCNTs 1…………………………35 2.3 De-bundling of (poly dC)- and (poly dT)-SWCNTs. …………………………35 2.4 Entwinement of (poly dN)-SWCNTs 1 by ssDNA 2……………………………36 2.5 Disassembly of ssDNA@(poly dN)-SWCNTs 3……………………………….40 2.6 Entwinement of (poly dN)-SWCNT 1 by (poly C)ssDNA 9. …………………...46 2.7 Synthesis of β-ketoester 16..…………….…………………………………...50 2.8 Synthesis of silicon-containing monomer 20...………………………………...51 2.9 Photolysis of ethyl 2-([dimethyl(phenyl)silyl]methyl)-5-[(4- methoxybenzyl)oxy]-3-oxopentanoate 20d……………………………………52 2.10 Photolysis of ethyl 6-[(4-methoxybenzyl)oxy]-3-oxo-2- [(trimethylsilyl)methyl]hexanoate 20e………………………………………….54 2.11 Synthesis of silicon-containing polymer 32……………………...……………...56 2.12 Photolysis of silicon-containing polymer 32……………………...……………..57 3. Discussion ………………………………………………………………………55 3.1 Model study of the SWCNT entwined with ssDNA…………………………...58 3.2 Biochemical Kit………………………………………………………………...60 3.3 Various strategies to obtain the β-ketoesters…………………………………...64 4. Conclusion ……………………………………………………………………...68 5. Experimental …………………………………………………………………...69 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6a…………………….………………………….…………………………………....71 5´-O-(9-Azido-4,7-dioxanonanyl)guanosine 6b.………….………………………....73 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxycytidine …………………………………………………………….………….74 5´-O-(9-Azido-4,7-dioxanonanyl)-2´-deoxycytidine……………….……………......75 (Poly dG)-SWCNT 1G …………………………………………..…………………..76 (Poly dC)-SWCNT 1C …………………………………….………………………...77 Standard Procedure 1 for the Synthesis of -ketoester…………...………………….80 Standard Procedure 2 for the Silylation of -ketoester ……………………………….80 Ethyl 4-[(4-methoxybenzyl)oxy]-3-oxobutanoate 16a……………………………….81 Ethyl 5-[(4-methoxybenzyl)oxy]-3-oxopentanoate 16b……...………………………82 Ethyl 6-[(4-methoxybenzyl)oxy]-3-oxohexanoate 16c………………………………82 Ethyl 4-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]butanoate 20a…..83 Ethyl 2-([dimethyl(phenyl)silyl]methyl)-4-[(4-methoxybenzyl)oxy]-3-oxobutanoate 20b……………………………………………………………………………………84 Ethyl 5-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]pentanoate 20c… 85 Ethyl 2-((dimethyl(phenyl)silyl)methyl)-5-((4-methoxybenzyl)oxy)-3-oxopentanoate 20d……………………………………………………………………………………86 Ethyl 6-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]hexanoate 20e…..87 Ethyl 2-[(dimethyl(phenyl)silyl)methyl]-6-[(4-methoxybenzyl)oxy]-3-oxohexanoate 20f………………………………………………………………………………….…88 6. References ……………………………………………………………………...90 7. Spectra 1H NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6a…………………….…………………...103 13C NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6a…………………….…………………...103 IR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6a………………………………..….……………………………..104 1H NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6b..…………………….………………….104 13C NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6b..…………………….………………….105 IR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine 6b..…………………….…………………………………………..105 1H NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxycytidine……..…………………….…………………..106 13C NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxycytidine..…………………….………………………..106 IR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-3´-O-(tert-butyl)dimethylsilyl-2´-deoxyguanosine ..……………………….…………………………………………..107 1H NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-2´-deoxycytidine……………………………..…………………….…………………..107 13C NMR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-2´-deoxycytidine..…………………….………………………………………………..108 IR of compound 5´-O-(9-Azido-4,7-dioxanonanyl)-2´-deoxycytidine ..……………………….…………………………………………….108 IR of compound (Poly dG)-SWCNT 1G ………………………..…………………109 IR of compound (Poly dC)-SWCNT 1C……………….…………….......................109 1H NMR of compound Ethyl 4-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]butanoate 20a………………………………………………110 13C NMR of compound Ethyl 4-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]butanoate 20a………………………………………………110 IR of compound Ethyl 4-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]butanoate 20a………………………………………………111 1H NMR of compound Ethyl 2-([dimethyl(phenyl)silyl]methyl)-4-[(4-methoxybenzyl)oxy]-3-oxobutanoate 20b...………………………………………..111 13C NMR of compound Ethyl 2-([dimethyl(phenyl)silyl]methyl)-4-[(4-methoxybenzyl)oxy]-3-oxobutanoate 20b..………………………………………..112 IR of compound Ethyl 2-([dimethyl(phenyl)silyl]methyl)-4-[(4-methoxybenzyl)oxy]-3-oxobutanoate 20b…………………………………………………………….…...112 1H NMR of compound Ethyl 5-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]pentanoate 20c……………………………………………..113 13C NMR of compound Ethyl 5-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]pentanoate 20c……………………………………………..113 IR of compound Ethyl 5-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]pentanoate 20c…………………………………………......114 1H NMR of compound Ethyl 2-((dimethyl(phenyl)silyl)methyl)-5-((4-methoxybenzyl)oxy)-3-oxopentanoate 20d……………………………………..…..114 13C NMR of compound Ethyl 2-((dimethyl(phenyl)silyl)methyl)-5-((4-methoxybenzyl)oxy)-3-oxopentanoate 20d…………………………………………115 IR of compound Ethyl 2-((dimethyl(phenyl)silyl)methyl)-5-((4-methoxybenzyl)oxy)-3-oxopentanoate 20d...………………………………………...................................115 1H NMR of compound Ethyl 6-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]hexanoate 20e………………………………………….…..116 13C NMR of compound Ethyl 6-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]hexanoate 20e…………………………………………...…116 IR of compound Ethyl 6-[(4-methoxybenzyl)oxy]-3-oxo-2-[(trimethylsilyl)methyl]hexanoate 20e………………………………………...........117 1H NMR of compound Ethyl 2-[(dimethyl(phenyl)silyl)methyl]-6-[(4-methoxybenzyl)oxy]-3-oxohexanoate 20f………………………………...…….…..117 13C NMR of compound Ethyl 2-[(dimethyl(phenyl)silyl)methyl]-6-[(4-methoxybenzyl)oxy]-3-oxohexanoate 20f……………………………………......…118 IR of compound Ethyl 2-[(dimethyl(phenyl)silyl)methyl]-6-[(4-methoxybenzyl)oxy]-3-oxohexanoate 20f...…………………………………………..……………...........118 List of Figures Figure 1. Types of carbon nanotubes...….......……………………………………... 1 Figure 2. Biomedical Applications of Pristine SWCNTs………………………….. 3 Figure 3. Various modifications of Pristine SWCNTs ……………………………...5 Figure 4. Functionalized SWCNT with Reduced Toxicity …………………………7 Figure 5. A biochemical rod…………………………………………………………9 Figure 6. Representative diagram of Nucleobase-Functionalized Carbon Nanotubes and the Pseudo Double Helix Formation with ssDNA………..12 Figure 7. Novel drug delivery strategies by nano biomaterials…………...………..27 Figure 8. Synthesis and characterization of functionalized biochemical rods….....30 Figure 9. Entwinement of functionalized biochemical rods ……………………….37 Figure 10. Effect of temperature, pH and sonication….……………………………41 Figure 11. Entwinement of functionalized SWCNT 1 with (poly C)ssDNA 9….....46 Figure 12. Represntative model of ssDNA@(poly dN)-SWCNT………………….59 Figure 13. Thermogravimetric analysis grafted SWCNTs………………………...62 List of Tables Table 1. Calculation of SWCNT diameter from radial breathing mode (RBM)…..34 Table 2. D band to G band ratio of the SWCNTs………………………………….35 Table 3. The molecular weight of polymer before and after photolysis…………...58 Table 4. Comparison of properties………………………………………………... 63 Table 5. Optimization conditions for the Silylation reaction……………………...65 List of Schemes Scheme 1. Entwinement of (poly dN)-SWCNT 1 with ssDNA 2………………….11 Scheme 2. Norrish Type photo-degradation of polymers………………………….14 Scheme 3. Norrish Type I cleavage of poly(butadienes)…………………………..15 Scheme 4. Photodegradable polyuria………………………………………………17 Scheme 5. Effect of Me3Si group………………………………………………….18 Scheme 6. Representative diagram of σ–π hyperconjugation………………..……19 Scheme 7. Norrish Type cleavage of ketone………………………………………20 Scheme 8. Representation of effect of silyl group………………………………....21 Scheme 9. Photolysis of 17-acetoxy-19-oxo-4-androsten-3-one…………………..23 Scheme 10. Decarbonylation by photolysis……………….……………………….23 Scheme 11. Silicon-directed decarbonylation induced by chemical reagents….….25 Scheme 12. Regioselective cleavage……………………………………………... 26 Scheme 13. Design of β-ketoesters with multiple photo cleavable sites…………..29 Scheme 14. Synthesis scheme of β-ketoester……………………………………...51 Scheme 15. Synthesis of silicon-containing monomer…………………………….52 Scheme 16. Photolysis and GC-MS analysis spectra after 1.5 h of UV irradiation of 20d…………………………………....………………………………53 Scheme 17. Photolysis and GC-MS analysis spectra after (a) 1.5 h of UV irradiation and (b) 2.0 h of 20e……………………………………...…………...55 Scheme 18. Synthesis of silicon containing polymer……………………………...57 Scheme 19. Photolysis of silicon containing polymer……………………………..58 Scheme 20. Trial 1 to synthesize 37……………………………………………….64 Scheme 21. Trial 2 to synthesize 39……………………………………………….65 Scheme 22. Competing reaction for alkylation at active methylene position……...66 Scheme 23. Trial 3 to synthesize 43……………………………………………….66 Scheme 24. Trial 4 to synthesize 48……………………………………………….67 Scheme 25. Trial 5 to synthesize 20c……………………………………………...68

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