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研究生: 林秉衡
Lin, Ping-Heng
論文名稱: 以邏輯閘建構全細胞生物感測器檢測銅離子
Development of Whole-cell biosensors based on Logic Gate to Detect Copper ion
指導教授: 葉怡均
Yeh, Yi-Chun
口試委員: 杜玲嫻
Tu, Ling-Hsien
蔡伸隆
Tsai, Shen-Long
葉怡均
Yeh, yi-chun
口試日期: 2023/06/27
學位類別: 碩士
Master
系所名稱: 化學系
Department of Chemistry
論文出版年: 2023
畢業學年度: 111
語文別: 中文
論文頁數: 118
中文關鍵詞: 全細胞生物感測器重金屬調控系統邏輯閘重組蛋白耐金屬貪銅菌大腸桿菌銅離子T7 RNA聚合酶
英文關鍵詞: Whole-Cell Biosensors (WCBs), Regulatory Systems, Metals, Logic Gate, Recombinant Proteins, Cupriavidus metallidurans,, E. coli, Copper ions
研究方法: 實驗設計法行動研究法準實驗設計法
DOI URL: http://doi.org/10.6345/NTNU202300979
論文種類: 學術論文
相關次數: 點閱:68下載:8
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  • 全細胞生物感測器是利用細菌作為感測器主體,透過基因工程技術,藉由賦予它不同調控基因組,使之具有檢測特定待測物的能力,其具有操作方便、價格低廉,對環境污染低等優點,使全細胞生物感測器越來越蓬勃發展。本論文是利用耐金屬貪銅菌 (Cupriavidus metallidurans, C. metallidurans) 作為宿主細菌,並且融入邏輯閘中的AND gate概念設計質體,希望利用兩個啟動子PCopA (Cu2+、Zn2+、Cd2+) 與PCopZ (Cu2+、Au3+、Ag+) 之間的交集,提高對銅離子的專一性,並且使用了Spy Tag/Catcher黏合標籤,提高重組sfCherry3C(1-10)、sfCherry3C(11)的效率以及重組T7 RNA聚合酶 (拆成C-T7和N-T7兩片段) 並作為訊號放大器,提高檢測銅離子的表現。在以上兩個系統,皆已成功建構出對銅離子專一的菌株,在兩系統中: sfCherry3C (2.5-250 μM) 、T7 RNAP (0.1-5 μM) 都有良好的線性,以及低偵測極限,但目前對於背景值以及檢測倍率的方面還需做進一步的優化。結論來說,我成功了開發了一個對銅離子專一的全細胞生物感測器,雖然目前的檢測表現還有進步空間,但可以利用此兩系統作為基礎,優化並發展出更完善的檢測器。

    Whole-cell biosensors (WBCs) utilize bacteria as hosts for detection. In order to detect environmental pollutants such as metal ions, I utilized genetic engineering techniques to introduce genes into bacteria to achieve our goal. WBCs are known for their low cost, simplicity, and environmentally friendly, which contribute to their rapid development. In my research, I employed C. metallidurans as the host organism and integrated the concept of an AND gate into plasmid design. I chose two promoters, PCopA (Cu2+, Zn2+, Cd2+) and PCopZ (Cu2+, Au3+, Ag+), to enhance the specificity of Cu2+ detection. Additionally, I introduced the recombinant tag Spy Tag/Catcher to improve the efficiency of complementation sfCherry3C(1-10), sfCherry3C(11), and fusion T7 RNA polymerase (C-T7/N-T7), serving as a signal amplifier to enhance Cu2+ detection performance. I successfully constructed Cu2+-specific strains in both of systems. The sfCherry3C system and T7 RNAP system exhibited good linear ranges of 2.5-250 μM and 0.1-5 μM, respectively. Despite their low limit of detection. Unfortunately, both of systems need to be further modified because of high background and low induction fold. In conclusion, I have successfully constructed Cu2+-specific WBCs utilizing the concept of an AND gate. Although optimization is necessary to enhance the detection performance of these two systems, they serve as a foundation for the future development of a more comprehensive detector.

    誌謝 i 中文摘要 ii Abstract iii 目錄 iv 圖目錄 viii 表目錄 x Chapter 1 Introduction 1 1-1基因工程 (Genetic engineering) 1 1-2全細胞生物感測器 (Whole-Cell Biosensor) 3 1-3 宿主細菌 (Host Cell) 4 1-3-1 大腸桿菌 (Escherichia coli, DH5α) 4 1-3-2 大腸桿菌 (Escherichia coli S17) 5 1-3-3 耐金屬貪銅菌 (Cupriavidus metallidurans CH34) 5 1-4 調控系統 6 1-4-1 MerR家族金屬調控系統 6 1-4-2 CueR 調控蛋白 (CueR regulatory system) 7 1-4-3 CopS/R二元調控系統 (CopS/R two-component system) 8 1-5邏輯閘 (Logic gate) 9 1-5-1 檢測目標 (銅二價離子) 10 1-5-2 Spy Tag/Spy Catcher 11 1-5-3 T7 RNA Polymerase (RNAP) 12 1-6 文獻回顧 13 1-6-1 銅離子感測器文獻 13 1-6-2 紅螢光蛋白sfCherry3C與Spy Tag/Spy Catcher相對位置的結合能力 15 Chapter 2 Experimental Materials and Equipment 17 2-1 實驗藥品 17 2-2 實驗儀器 19 Chapter 3 Experimental Methods 21 3-1 基因克隆 (Genetic cloning) 21 3-2 畫盤 (Plate streaking) 21 3-3 菌液培養 (Pre-culture) 22 3-4 質體萃取 (Plasmid extraction) 22 3-5 聚合酶連鎖反應 (Polymerase Chain Reaction, PCR) 23 3-6 引子黏合 (Oligo) 24 3-7 限制酶剪切 (Restriction enzyme digestion) 25 3-8 膠體電泳 (Agarose gel electrophoresis) 26 3-9 連接作用 (Ligation) 26 3-10 建構方法 (Construction methods) 27 3-10-1 Golden gate assembly 27 3-10-2 Gibson assembly 28 3-10-3 KLD (Kinase/Ligase/DpnI) 29 3-11 轉形作用 (Transformation) 29 3-12 勝任細胞 (Competent cell) 30 3-13 定序 (Sequencing) 31 3-14 存菌 (Storage of the bacteria) 31 3-15 接合作用 (Conjugation) 32 Chapter 4 Experimental Design 32 4-1 質體建構 32 4-1-1 銅離子感測器設計概念 33 4-2 實驗步驟 34 4-2-1 培養過程 34 4-2-2 數據處理 35 Chapter 5 Results and Discussions 36 5-1 銅離子感測器 36 5-1-1 Spy Tag/Catcher系統 36 5-1-1-1 啟動子PCopA和PCopZ金屬誘導性測驗 36 5-1-1-2 單一分裂紅螢光蛋白螢光測試 37 5-1-1-3 Spy Tag/Catcher系統的銅離子初步檢測 38 5-1-1-4 利用抗生素驗證啟動子洩漏表達的問題 40 5-1-1-5 Spy Tag/Catcher系統檢測銅離子以及金離子的檢量線 42 5-1-1-6 YCY_1482真實樣品檢測 44 5-1-1-7 YCY_1482金屬干擾性實驗 45 5-1-1-8 YCY_1482紅螢光顯微鏡圖 46 5-1-2 C-T7/N-T7系統 48 5-1-2-1 C-T7/N-T7基因位置的篩選 48 5-1-2-1-1 C-T7和Spy Tag基因順序優化 48 5-1-2-1-2 對調啟動子(PCopA/PCopZ) 50 5-1-2-1-3 C-T7/N-T7與黏合標籤 (Spy Tag/Catcher) 的交換 52 5-1-2-1-4 Spy Tag-C-T7與Spy Catcher-N-T7在不同啟動子後的比較 54 5-1-2-2 衍生菌株銅、金離子的金屬干擾性實驗 56 5-1-2-3 最佳菌株YCY_1577金屬干擾性實驗 59 5-1-2-4最佳菌株YCY_1577檢量線 60 5-1-2-5 最佳菌株YCY_1577真實樣品檢測 61 5-1-2-6 最佳菌株YCY_1577紅螢光顯微鏡圖 62 5-1-2-7 最佳菌株YCY_1577將PT7-RBS-RFP-T換至PCopA後面的數據表現 63 Chapter 6 Conclusion 64 附錄 66 本篇建構的質體圖 89 Reference 112

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