改良二氧化矽纖維膜分離程序於培養的細胞中微核醣核酸之純化

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：28

、訪客IP：18.224.64.226

姓名

陳昱圻(Yu-Chi Chen) 查詢紙本館藏

畢業系所

化學工程與材料工程學系

論文名稱

改良二氧化矽纖維膜分離程序於培養的細胞中微核醣核酸之純化
(Improved sample preparation process for miRNA isolation from the culture cells by using silica fiber membrane)

相關論文

★ 類澱粉胜肽聚集行為之電腦模擬	★ 溶解度參數計算及量測於HPLC純化胜肽程序之最佳化研究
★ 利用恆溫滴定微卡計量測蛋白質分子於溶液中之第二維里係數與自我聚集之行為	★ 利用SPRi探討中性DNA探針相較於一般DNA探針在低鹽雜交環境下之優勢
★ 矽奈米線場效電晶體多點之核酸檢測研究	★ 使用不帶電中性核酸探針於矽奈米線場效電晶體檢測去氧核醣核酸與微核醣核酸之研究
★ 運用nDNA 修飾引子於PCR及qPCR平台以提升專一性之研究	★ 設計中性DNA引子及探針以提升PCR與qPCR專一性之研究
★ 使用中性不帶電去氧核醣核酸探針於矽奈米線場效電晶體檢測微核醣核酸之研究	★ 使用不帶電中性核酸探針於原位雜交技術檢測微核醣核酸之研究
★ 設計不帶電中性核酸探針於矽奈米線場效電晶體來改善富含GC鹼基核醣核酸之檢測專一性	★ 合成5’-MeNPOC-2’-deoxynucleoside p-methoxy phosphoramidite以作為應用於原位合成之新穎性中性核苷酸之研究
★ 立體紙基外泌體核酸萃取裝置應用於檢測不同微環境下癌細胞所釋放之外泌體與外泌體微小核醣核酸之表現量	★ 利用抗原結合區段之抗體片段探針於矽奈米線場效電晶體來改善抗原檢測濃度極限之研究
★ 利用表面電漿共振影像儀驗證最適化之抗非專一性吸附場效電晶體表面於血清環境下之免疫測定	★ 使用混合自組裝單層膜於矽奈米線場效電晶體檢測微小核醣核酸之研究

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

[檢視]

[下載]

本電子論文使用權限為同意立即開放。
已達開放權限電子全文僅授權使用者為學術研究之目的，進行個人非營利性質之檢索、閱讀、列印。
請遵守中華民國著作權法之相關規定，切勿任意重製、散佈、改作、轉貼、播送，以免觸法。

摘要(中)

微小核醣核酸(microRNAs)近年來被發現在許多疾病的診斷與治療是很有前景的的生物標誌分子。對於微小核醣核酸的核酸在臨床的分析中，待測樣本的純度與品質是很重要的，如果在分析前萃取微小核醣核酸有差異或汙染，會造成分析結果的變異數增加使醫療資訊判斷錯誤。在此研究中，我們改良了市售的核醣核酸萃取套組並期望增加從細胞培養的細胞中萃取出微小核醣核酸的穩定的回收量與標準化。首先，我們探討核醣核酸與二氧化矽純化管柱裡的二氧化矽纖維與核酸間的結合機制，發現在較低的pH值且有離散劑(chaotropic agent)、二價陽離子與醇類的溶液中，核醣核酸會較容易與二氧化矽表面吸附結合，改變這些溶液中的條件能增加核醣核酸吸附在二氧化矽表面的結果。對於核酸脫附二氧化矽表面的條件，增加溫度與增加洗脫液的pH值能增強二氧化矽表面與核醣核酸間的排斥力，進而增加核醣核酸脫附於二氧化矽表面的量。為了要檢測與定量微小核醣核酸是否會受到上述參數影響，我們使用毛細管凝膠電泳(capillary gel electrophoresis)與及時聚合?連鎖反應(Real-time polymerase chain reaction)與矽奈米線場效電晶體生物感測器( nanowire field effect transistor biosensor )當作檢測工具，並同時使用內源性與外源性的微小核醣核酸當作評估的標準，比較改良後的萃取套組與改良前的萃取套組的萃取效率。

相較於原始的萃取套組，發現在使用了Tris-HCl EDTA buffer (Tris HCl 20mM , EDTA 2mM)改變洗脫時的pH值至pH 8並調高洗脫時的溫度，造成微小核醣核酸與二氧化矽表面間的負電排斥力，因而增加微小核醣核酸的脫附效率；另外加入二價鈣離子並不會增加微小核醣核酸的萃取效率，因為在pH 5.5左右，二氧化矽表面的負電荷不足，鈣離子形成鹽橋的能力有限；而增加溶液中酒精的濃度至65%體積百分比，微小核醣核酸的回收效率比60%體積百分比與70%體積百分比要來的好。最後把得到的最適條件組合起來成改良後的萃取套組，發現改良過後的萃取套組能夠增加內源性miR-21與外源性miR-39微小核醣核酸的回收率初步估算為4至6倍。另一方面，使用正在發展中的矽奈米線場效電晶體生物感測器檢測微小核醣核酸的檢測結果，發現矽奈米線場效電晶體能夠辨別出在細胞萃取物中目標基因的濃度差別，是很有展望的核酸萃取工具。

摘要(英)

MicroRNAs (miRNAs) are promising biomarkers that could be applied on the diagnosis and treatment of different diseases. For the miRNA diagnosis assays, the purity and quality of miRNA samples are important in pre-analytical steps. In this study, we modified the commercial RNA isolation kits for miRNA extraction from the culture cell to improve the purity and amount of miRNA. First of all, we investigated the binding mechanism of nucleic acid and silica membrane of silica spin column. Consequently, we found that nucleic acid are much easier binding with silica surface at low pH value, presence of chaotropic salt and alcohol solution condition. Moreover, there are several methodologies could increase the binding affinity between RNA and silica surface. In these methodologies, adjusting the solution polarity, and adding divalent cation in binding process can promote RNA adsorption on silica surface. For desorption, we raised the elution temperature to break the bonding and raise the pH value to enhance the repulsive force between RNA and silica membrane to increase the RNA recovery. By using the real-time polymerase chain reaction (RT-qPCR) and nanowire field effect transistor (NWFET), we could compare the relative ef?ciencies of modified protocol and the original one. Using spike-in synthesis exogenous miRNA, mir-39, evaluate the recovery of modified process.
　The result show that using the TE buffer for the elution buffer and increasing the elute temperature will increasing the miRNA isolation efficiency. Moreover, the presence of the Ca2+ cation did not improve the miRNA isolation process. The ethanol concentration 65% (v/v) for miRNA isolation have the better efficiency than the 60% (v/v) and 70% (v/v). In the end, we combine three results as the new protocol, the new protocol isolation efficiency is 2 fold better than the original protocol. The NWFET was applied to detect the miRNA, the result was compared with the RT-qPCR for miRNA quantification. The result showed that the NWFET can distinguish different concentration of target miRNA in the cell extraction. As for the result, the NWFET is the potential tool for detecting the miRNA.

關鍵字(中)

★ miRNA萃取
★ 二氧化矽吸附RNA
★ RNA萃取套組改良

關鍵字(英)

★ miRNA extraction
★ silica adsorption RNA

論文目次

目錄

摘要 i
Abstract iii
誌謝 v
目錄 vi
圖目錄 x
表目錄 xiii
第一章緒論 1
第二章　文獻回顧 3
2.1核酸分子 3
2.1.1核酸分子介紹 3
2.1.2去氧核醣核酸 4
2.1.3核醣核酸 7
2.1.4微小核醣核酸 7
2.2生物標記與核酸檢體 9
2.2.1生物標記的定義與作用 9
2.2.2核酸檢體種類與處理 10
2.2.3液態切片與核酸生物標記 11
2.3核酸萃取 12
2.3.1核酸萃取發展 12
2.3.2液相萃取 13
2.3.3固相萃取 13
2.3.4萃取套組的比較 14
2.3.5 自動核酸萃取發展 16
2.4 核酸純化與二氧化矽管柱 17
2.4.1固相吸附 17
2.4.2二氧化矽表面與核酸的吸附機制 18
2.5 RNA萃取品質控管( Quality Control) 23
2.5.1 分光光度計檢測 23
2.5.2 使用毛細管凝膠電泳量測RNA片段分佈 25
2.6 即時聚合?鏈式反應 ( qPCR )之方法 27
2.6.1即時聚合?鏈式反應 ( qPCR )檢測miRNA原理 27
2.6.2 miRNA的定量與標準化 31
2.7 使用場效電晶體生物感測器檢測核酸 32
2.7.1場效電晶體生物感測器原理 32
2.7.2 晶片表面改質 35
第三章實驗藥品、儀器設備與方法 38
3.1 實驗藥品與材料 38
3.1.1細胞培養 38
3.1.2核酸萃取 38
3.1.3反轉錄即時聚合?鏈式反應 39
3.1.4晶片表面改質 39
3.2儀器設備 40
3.3 實驗方法 40
3.3.1 細胞培養 40
3.3.2 微小核醣核酸萃取 42
3.3.3反轉錄即時聚合?鏈式反應 44
3.3.4. COB(circuit on board)晶片表面改質 46
3.3.5 矽奈米線場效電晶體生物感測器電性測量 48
3.3.6 毛細管膠體電泳 49
3.3.7 自動核酸純化儀 50
第四章結果與討論 51
4.1 miRNA萃取優化 51
4.2 使用自動核酸純化儀萃取miRNA 53
4.3使用毛細管電泳分析miRNA變化量 54
4.4 使用qPCR分析miRNA變化量 56
4.4.1 改變萃取時的洗脫溫度 56
4.4.2 改變洗脫時的pH值 58
4.4.3 加入二價鈣離子對萃取的影響 61
4.4.4 改變核酸吸附時的酒精濃度 62
4.4.5 改良優化原始的核酸萃取步驟 64
4.5 使用qPCR做miRNA絕對定量 66
4.6使用矽奈米線場效電晶體檢測微小核醣核酸 67
第五章結論與未來展望 72
5.1結論 72
5.2未來展望 73
第六章參考文獻 74

參考文獻

1. Dahm, R., Friedrich Miescher and the discovery of DNA. Dev Biol, 2005. 278(2): p. 274-88.
2. Watson, J.D. and F.H. Crick, Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 1953. 171(4356): p. 737-8.
3. Higgs, P.G., RNA secondary structure: physical and computational aspects. Q Rev Biophys, 2000. 33(3): p. 199-253.
4. Tan, S.C. and B.C. Yiap, DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol, 2009. 2009: p. 574398.
5. Walleshauser, J.G., Kessler, T., Morse, D.E., Tannous, B.A., & Chiu, N.H, A Simple Approach for Evaluating Total MicroRNA Extraction from Mouse Brain Tissues. 2013.
6. PBartel, D., MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell. 2004 Jan 23, 2004. 116(2): p. 281-297.
7. Ian G. Cannell, Y.W.K., Martin Bushell,, How do microRNAs regulate gene expression? Biochem Soc Trans, 2008.
8. Macfarlane, L.A. and P.R. Murphy, MicroRNA: Biogenesis, Function and Role in Cancer. Curr Genomics, 2010. 11(7): p. 537-61.
9. Hutvagner, G. and P.D. Zamore, A microRNA in a multiple-turnover RNAi enzyme complex. Science, 2002. 297(5589): p. 2056-60.
10. Peng, Y. and C.M. Croce, The role of MicroRNAs in human cancer. Signal Transduction And Targeted Therapy, 2016. 1: p. 15004.
11. Davidson-Moncada, J., F.N. Papavasiliou, and W. Tam, MiRNAs of the Immune System: Roles in Inflammation and Cancer. Annals of the New York Academy of Sciences, 2010. 1183: p. 183-194.
12. The Basics: RNase Control:Avoiding, Detecting, and Inhibiting RNase. 2012; Available from:https://www.thermofisher.com/tw/zt/home/references/ambion-tech-support/nuclease-enzymes/general-articles/the-basics-rnase-control.html.
13. Samadani, A.A., et al., RNA Extraction from Animal and Human′s Cancerous Tissues: Does Tissue Matter? International Journal of Molecular and Cellular Medicine, 2015. 4(1): p. 54-59.
14. Gibbings, D.J., et al., Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol, 2009. 11(9): p. 1143-9.
15. Azmi, A.S., B. Bao, and F.H. Sarkar, Exosomes in Cancer Development, Metastasis and Drug Resistance: A Comprehensive Review. Cancer metastasis reviews, 2013. 32(0): p. 10.1007/s10555-013-9441-9.
16. Chomczynski, P. and N. Sacchi, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem, 1987. 162(1): p. 156-9.
17. Avison, M.B., Measuring Gene Expression, ed. s. edition. 2007, New York: Taylor & Francis Group.
18. Xu, L., et al., Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts. Analytical Biochemistry, 2011. 419(2): p. 309-316.
19. Boom, R., et al., Rapid and simple method for purification of nucleic acids. J Clin Microbiol, 1990. 28(3): p. 495-503.
20. Brunet-Vega, A., et al., Variability in microRNA recovery from plasma: Comparison of five commercial kits. Analytical Biochemistry, 2015. 488: p. 28-35.
21. Sourvinou, I.S., A. Markou, and E.S. Lianidou, Quantification of circulating miRNAs in plasma: effect of preanalytical and analytical parameters on their isolation and stability. J Mol Diagn, 2013. 15(6): p. 827-34.
22. Duy, J., et al., Optimized microRNA purification from TRIzol-treated plasma. BMC Genomics, 2015. 16: p. 95.
23. Ning Suna, b., c,1, Congliang Dengb,1, Yi Liub, Xiaoli Zhaob, Yan Tangc, Renxiao Liuc, Qiang Xiaa,?, Wenlong Yand,e, Guanglu Ge, Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: Application to viral nucleic acid extraction from serum. Journal of Chromatography A, 2013.
24. O′Reilly, J.P., et al., Interfacial pH at an Isolated Silica?Water Surface. Journal of the American Chemical Society, 2005. 127(6): p. 1632-1633.
25. Vandeventer, P.E., et al., Multiphasic DNA Adsorption to Silica Surfaces under Varying Buffer, pH, and Ionic Strength Conditions. The Journal of Physical Chemistry B, 2012. 116(19): p. 5661-5670.
26. KATHRYN A. MELZAK, C.S.S., ROBIN F. B. TURNER,* AND CHARLES A. HAYNES, Driving Forces for DNA Adsorption to Silica in Perchlorate Solutions. COLLOID AND INTERFACE SCIENCE, February 26, 1996. 181: p. 635–644
27. Lei Xu , J.L., Liefeng Ling , Peng Wang , Ping Song , Ruirui Su , Guoping Zhu Altered nucleic acid partitioning during phenol extraction or silica adsorption
by guanidinium and potassium salts. Analytical Biochemistry, 2011.
28. Romanowski, G., et al., Persistence of Free Plasmid DNA in Soil Monitored by Various Methods, Including a Transformation Assay. Applied and Environmental Microbiology, 1992. 58(9): p. 3012-3019.
29. Nguyen, T.H. and M. Elimelech, Plasmid DNA adsorption on silica: kinetics and conformational changes in monovalent and divalent salts. Biomacromolecules, 2007. 8(1): p. 24-32.
30. Franchi, M., J.P. Ferris, and E. Gallori, Cations as mediators of the adsorption of nucleic acids on clay surfaces in prebiotic environments. Orig Life Evol Biosph, 2003. 33(1): p. 1-16.
31. Shen, Y., et al., Influence of solution chemistry on the deposition and detachment kinetics of RNA on silica surfaces. Colloids and Surfaces B: Biointerfaces, 2011. 82(2): p. 443-449.
32. Glasel, J.A., Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios. Biotechniques, 1995. 18(1): p. 62-3.
33. Farrell, R.E., Chapter 6 - Quality Control for RNA Preparations, in RNA Methodologies (Fourth Edition), R.E. Farrell, Editor. 2010, Academic Press: San Diego. p. 139-154.
34. Schroeder, O.M.S.L.A., RNA Integrity Number ( RIN ) – Standardization of RNA Quality Control. 2004.
35. Redshaw, N., et al., A comparison of miRNA isolation and RT-qPCR technologies and their effects on quantification accuracy and repeatability. Biotechniques, 2013. 54(3): p. 155-64.
36. Chugh, P. and D.P. Dittmer, Potential pitfalls in microRNA profiling. Wiley Interdiscip Rev RNA, 2012. 3(5): p. 601-16.
37. Mestdagh, P., et al., A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol, 2009. 10(6): p. R64.
38. Tsai, C.C., et al., Surface potential variations on a silicon nanowire transistor in biomolecular modification and detection. Nanotechnology, 2011. 22(13): p. 135503.
39. Chen, K.-I., B.-R. Li, and Y.-T. Chen, Silicon nanowire field-effect transistor-based biosensors for biomedical diagnosis and cellular recording investigation. Nano Today, 2011. 6(2): p. 131-154.
40. Li, Z., et al., Sequence-Specific Label-Free DNA Sensors Based on Silicon Nanowires. Nano Letters, 2004. 4(2): p. 245-247.
41. Niemeyer, C.M., Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl, 2010. 49(7): p. 1200-16.
42. Rusmini, F., Z. Zhong, and J. Feijen, Protein immobilization strategies for protein biochips. Biomacromolecules, 2007. 8(6): p. 1775-89.
43. Zaporozhchenko, I.A., et al., A phenol-free method for isolation of microRNA from biological fluids. Anal Biochem, 2015. 479: p. 43-7.
44. Smerkova, K., et al., Investigation of interaction between magnetic silica particles and lambda phage DNA fragment. Journal of Pharmaceutical and Biomedical Analysis, 2013. 86: p. 65-72.
45. Li, Y. and R.R. Breaker, Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group. Journal of the American Chemical Society, 1999. 121(23): p. 5364-5372.
46. (WPI), W.P.I., Debye-length-Multi-scale modeling and simulation of field-effect
nano-biosensors. 2008: Vienna.
47. Wang, Y.-H., Using neutralized-DNA on silicon nanowire field-effect transistor for microRNA detection, in Department of Chemical and Materials Engineering. 2017, National Central University.
48. Ramon-Nunez, L.A., et al., Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation. PLOS ONE, 2017. 12(10): p. e0187005.

指導教授

陳文逸(Wen-Yi Chen)

審核日期

2018-8-20

推文