| 研究生: |
王柏盛 Wang, Po-Sheng |
|---|---|
| 論文名稱: |
tmigd1基因單核苷酸多型性乾式檢測之試紙參數的最佳化與基因再現性測試 Optimization of Dry-Reagent Strip Biosensor and Reproducibility for Single Nucleotide Polymorphism in tmigd1 Gene |
| 指導教授: |
郭瑞昭
Kuo, Jui-Chao |
| 學位類別: |
碩士 Master |
| 系所名稱: |
工學院 - 材料科學及工程學系 Department of Materials Science and Engineering |
| 論文出版年: | 2017 |
| 畢業學年度: | 105 |
| 語文別: | 中文 |
| 論文頁數: | 141 |
| 中文關鍵詞: | 單核苷酸多型性 、免疫層析法 、奈米金 、菜鴨 |
| 外文關鍵詞: | single nucleotide polymorphism, lateral flow immunoassay, gold nanoparticle, Tsaiya duck |
| 相關次數: | 點閱:96 下載:4 |
| 分享至: |
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本論文之乾式檢測試紙系統應用於菜鴨之tmigd1基因之單核苷酸多型性(Single Nucleotide Polymorphism)檢驗,為先前研究初步測試開發可行之試紙檢測系統之延續研究,其免疫層析試紙主要藉由修飾核酸探針之奈米金粒子作為顯色單元,並使用鏈親和素(Streptavidin)作為試紙測試帶之探針,捕抓Primer Extension (PEXT)反應中對應SNP位置被延長而引入Biotin-16-dUTP之產物。
本論文針對試紙的特性研究分為兩個部份,分別為再現性測試與試紙參數最佳化實驗。在再現性測試實驗中,使用6組萃取自不同鴨隻之DNA樣品進行SNP檢測。其測試結果顯示出G/G基因型之試紙訊號特異性較A/A基因型為佳,且由肉眼觀察到每組試紙皆有明顯之假陽性(False Positive)訊號的產生。而在不添加PEXT產物之試紙測試中,發現到非特異性吸附之假陽性訊號的出現。
因此在試紙參數最佳化實驗,藉由調整試紙參數最佳化的測試來完全消除非特異性吸附之訊號。試紙的吸附強度訊號會受到試紙中參數的影響。故此,針對硝化纖維薄膜的孔徑(Pore Size)大小、奈米金粒子的用量以及Streptavidin的施加量進行調控,同時結合影像分析軟體ImageJ對吸附訊號進行強度的計算,得到完全消除非特異性吸附訊號之試紙參數。
最後,使用前述實驗所獲得之6組無非特異性吸附訊號之試紙參數,再使用一組G/G基因型與一組A/A基因型DNA樣品進行再現性測試。最終獲得最佳化之參數為15 μm的孔徑薄膜,奈米金用量為3 μL以及0.08 μg的Streptavidin施加量,完整的檢測時間5分鐘,即可得到偵測訊號結果。
In this research, we did the reproducibility test of dry-reagent strip biosensor for SNP detection in tmigd1 gene of Tsaiya duck (Anas platyrhynchos), and optimized the parameters of the strip.
The SNP detection system combined primer extension (PEXT) method with the lateral flow immunoassay for SNP discrimination. To validate the reproducibility of dry-reagent strip, we conducted the tests with 6 DNA samples. According to our results, the signal specificity of the strip detection was better for G/G genotype than A/A genotype samples. In addition, we found the appearance of false positive signal in every strip test results, and even affected the interpretation of the SNP detection results by naked eyes.
Therefore, we tried to control the pore size of the nitrocellulose membrane, gold nanoparticle usage and loading amount of streptavidin to eliminating the false positive signal without the addition of PEXT product. We got 6 sets of parameters of the strip, and then applied these strips to SNP detection. According to the detection results, we obtained the optimal strip parameter set for using 15 μm pore size of the membrane, 3 μL usage of gold nanoparticle and 0.08 μg loading amount of streptavidin.
1. A. J. Brookes, The essence of SNPs. Gene, 1999. 234: p. 177-186.
2. I. H. Consortium, A haplotype map of the human genome. Nature, 2005. 437: p. 1299-1320.
3. W. J. Strittmatter and A. D. Roses, Apolipoprotein E and Alzheimer's disease. Annual review of neuroscience, 1996. 19: p. 53-77.
4. H. L. Huang, Y. S. Cheng, C. W. Huang, M. C. Huang, and W. H. Hsu, A novel genetic marker of the ovomucoid gene associated with hatchability in Tsaiya ducks (Anas platyrhynchos). Animal genetics, 2011. 42: p. 421-427.
5. R. S. Herbst, J. V. Heymach, and S. M. Lippman, Molecular origins of cancer: Lung cancer. New England Journal of Medicine, 2008. 359: p. 1367-1380.
6. Y. Tanaka, N. Nishida, M. Sugiyama, M. Kurosaki, K. Matsuura, N. Sakamoto, M. Nakagawa, M. Korenaga, K. Hino, S. Hige, Y. Ito, E. Mita, E. Tanaka, S. Mochida, Y. Murawaki, M. Honda, A. Sakai, Y. Hiasa, S. Nishiguchi, A. Koike, I. Sakaida, M. Imamura, K. Ito, K. Yano, N. Masaki, F. Sugauchi, N. Izumi, K. Tokunaga, and M. Mizokami, Genome-wide association of IL28B with response to pegylated interferon-α and ribavirin therapy for chronic hepatitis C. Nature Genetics, 2009. 41: p. 1105-1109.
7. I. K. Litos, P. C. Ioannou, T. K. Christopoulos, J. Traeger-Synodinos, and E. Kanavakis, Genotyping of Single-Nucleotide Polymorphisms by Primer Extension Reaction in a Dry-Reagent Dipstick Format. Analytical Chemistry, 2007. 79: p. 395-402.
8. R. Dahm, Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Human Genetics, 2008. 122: p. 565-581.
9. J. J. P. B.R. Glick, C.L. Patten, Molecular biotechnology: Principles and applications of recombinant DNA. 2010, Washington, DC: ASM Press.
10. J. D. Watson and F. H. C. Crick, Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 1953. 171: p. 737-738.
11. J. SantaLucia, Jr. and D. Hicks, The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct, 2004. 33: p. 415-440.
12. F. Sanger and A. R. Coulson, A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 1975. 94: p. 441-448.
13. J. C. Venter, M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, H. O. Smith, M. Yandell, C. A. Evans, R. A. Holt, J. D. Gocayne, P. Amanatides, R. M. Ballew, D. H. Huson, J. R. Wortman, Q. Zhang, C. D. Kodira, X. H. Zheng, L. Chen, M. Skupski, G. Subramanian, P. D. Thomas, J. Zhang, G. L. Gabor Miklos, C. Nelson, S. Broder, A. G. Clark, J. Nadeau, V. A. McKusick, N. Zinder, A. J. Levine, R. J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A. E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T. J. Heiman, M. E. Higgins, R. R. Ji, Z. Ke, K. A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G. V. Merkulov, N. Milshina, H. M. Moore, A. K. Naik, V. A. Narayan, B. Neelam, D. Nusskern, D. B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M. L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y. H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N. N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J. F. Abril, R. Guigo, M. J. Campbell, K. V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y. H. Chiang, M. Coyne, C. Dahlke, A. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Venter, M. Wang, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh and X. Zhu, The sequence of the human genome. Science, 2001. 291: p. 1304-1351.
14. X. Chen and P. F. Sullivan, Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J, 2003. 3: p. 77-96.
15. R. K. Saiki, S. Scharf, F. Faloona, K. B. Mullis, G. T. Horn, H. A. Erlich, and N. Arnheim, Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 1985. 230: p. 1350-1354.
16. C. M. Plotz and J. M. Singer, The latex fixation test. I. Application to the serologic diagnosis of rheumatoid arthritis. Am J Med, 1956. 21: p. 888-892.
17. S. A. Berson and R. S. Yalow, Quantitative aspects of the reaction between insulin and insulin-binding antibody. Journal of Clinical Investigation, 1959. 38: p. 1996-2016.
18. E. Engvall and P. Perlmann, Enzyme-linked immunosorbent assay (ELISA) quantitative assay of immunoglobulin G. Immunochemistry, 1971. 8: p. 871-874.
19. D. P. Kalogianni, L. M. Boutsika, P. G. Kouremenou, T. K. Christopoulos, and P. C. Ioannou, Carbon nano-strings as reporters in lateral flow devices for DNA sensing by hybridization. Analytical and bioanalytical chemistry, 2011. 400: p. 1145-1152.
20. E. A. Sapountzi, S. S. Tragoulias, D. P. Kalogianni, P. C. Ioannou, and T. K. Christopoulos, Lateral flow devices for nucleic acid analysis exploiting quantum dots as reporters. Analytica chimica acta, 2015. 864: p. 48-54.
21. D. P. Kalogianni, I. K. Litos, T. K. Christopoulos, and P. C. Ioannou, Dipstick-type biosensor for visual detection of DNA with oligonucleotide-decorated colored polystyrene microspheres as reporters. Biosensors and Bioelectronics, 2009. 24: p. 1811-1815.
22. K. Glynou, P. C. Ioannou, T. K. Christopoulos, and V. Syriopoulou, Oligonucleotide-functionalized gold nanoparticles as probes in a dry-reagent strip biosensor for DNA analysis by hybridization. Anal Chem, 2003. 75: p. 4155-4160.
23. F. Papanikos, A. Iliadi, M. Petropoulou, P. C. Ioannou, T. K. Christopoulos, E. Kanavakis, and J. Traeger-Synodinos, Lateral flow dipstick test for genotyping of 15 beta-globin gene (HBB) mutations with naked-eye detection. Analytica chimica acta, 2012. 727: p. 61-66.
24. H. Y. T. Raphael C. Wong, ed. Lateral Flow Immunoassay. 1 ed. 2009, Humana Press: New York. XII, 224.
25. C. A. Mirkin, R. L. Letsinger, R. C. Mucic, and J. J. Storhoff, A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature, 1996. 382: p. 607-609.
26. S. J. Hurst, A. K. Lytton-Jean, and C. A. Mirkin, Maximizing DNA loading on a range of gold nanoparticle sizes. Anal Chem, 2006. 78: p. 8313-8318.
27. 林志韋, tmigd1基因單核苷酸多型性之乾式生物檢測試紙系統. 國立成功大學材料科學及工程學系碩士論文, 2016.
28. D. P. Kalogianni, S. Goura, A. J. Aletras, T. K. Christopoulos, M. G. Chanos, M. Christofidou, A. Skoutelis, P. C. Ioannou, and E. Panagiotopoulos, Dry reagent dipstick test combined with 23S rRNA PCR for molecular diagnosis of bacterial infection in arthroplasty. Anal Biochem, 2007. 361: p. 169-175.
29. J. M. Cooper, J. Shen, F. M. Young, P. Connolly, J. R. Barker, and G. Moores, The imaging of streptavidin and avidin using scanning tunnelling microscopy. Journal of Materials Science: Materials in Electronics, 1994. 5: p. 106-110.
30. L. Välimaa, Streptavidin-a versatile binding protein for solid-phase immunoassays. 2008. (Doctoral dissertation, Turku University)
31. P. G. Zerefos, P. C. Ioannou, J. Traeger‐Synodinos, G. Dimissianos, E. Kanavakis, and T. K. Christopoulos, Photoprotein aequorin as a novel reporter for SNP genotyping by primer extension–application to the variants of mannose‐binding lectin gene. Human mutation, 2006. 27: p. 279-285.
32. D. K. Toubanaki, T. K. Christopoulos, P. C. Ioannou, and A. Gravanis, Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis Communicated by Ulf Landegren. Human mutation, 2008. 29: p. 1071-1078.
33. I. K. Litos, P. C. Ioannou, T. K. Christopoulos, J. Traeger-Synodinos, and E. Kanavakis, Multianalyte, dipstick-type, nanoparticle-based DNA biosensor for visual genotyping of single-nucleotide polymorphisms. Biosensors and Bioelectronics, 2009. 24: p. 3135-3139.
34. Y. He, K. Zeng, A. S. Gurung, M. Baloda, H. Xu, X. Zhang, and G. Liu, Visual detection of single-nucleotide polymorphism with hairpin oligonucleotide-functionalized gold nanoparticles. Analytical chemistry, 2010. 82: p. 7169-7177.
35. J. Li, D. McMillan, and J. Macdonald, Enhancing the Signal of Lateral Flow Immunoassays by Using Different Developing Methods. Sensors and Materials, 2015. 27: p. 549-561.
36. Z. Xiao, P. Lie, Z. Fang, L. Yu, J. Chen, J. Liu, C. Ge, X. Zhou, and L. Zeng, A lateral flow biosensor for detection of single nucleotide polymorphism by circular strand displacement reaction. Chemical Communications, 2012. 48: p. 8547-8549.
37. I. K. Litos, E. Emmanouilidou, K. M. Glynou, E. Laios, P. C. Ioannou, T. K. Christopoulos, M. Kampa, E. Castanas, and A. Gravanis, Rapid genotyping of CYP2D6, CYP2C19 and TPMT polymorphisms by primer extension reaction in a dipstick format. Analytical and bioanalytical chemistry, 2007. 389: p. 1849-1857.
38. X. Zhang, M. R. Servos, and J. Liu, Instantaneous and quantitative functionalization of gold nanoparticles with thiolated DNA using a pH-assisted and surfactant-free route. Journal of the American Chemical Society, 2012. 134: p. 7266-7269.
39. K. Saha, S. S. Agasti, C. Kim, X. Li, and V. M. Rotello, Gold nanoparticles in chemical and biological sensing. Chemical reviews, 2012. 112: p. 2739-2779.
40. A. Ahmad, S. Low, and S. A. Shukor, Effects of membrane cast thickness on controlling the macrovoid structure in lateral flow nitrocellulose membrane and determination of its characteristics. Scripta materialia, 2007. 57: p. 743-746.
41. B. T. Kurien and R. H. Scofield, Protein blotting: a review. Journal of immunological methods, 2003. 274: p. 1-15.
42. J. Yguerabide and E. E. Yguerabide, Light-scattering submicroscopic particles as highly fluorescent analogs and their use as tracer labels in clinical and biological applications: I. Theory. Analytical biochemistry, 1998. 262: p. 137-156.
43. E. Prodan, C. Radloff, N. J. Halas, and P. Nordlander, A hybridization model for the plasmon response of complex nanostructures. science, 2003. 302: p. 419-422.
44. C. Sönnichsen, B. M. Reinhard, J. Liphardt, and A. P. Alivisatos, A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nature biotechnology, 2005. 23: p. 741-745.
45. P. Mulvaney, Surface plasmon spectroscopy of nanosized metal particles. Langmuir, 1996. 12: p. 788-800.
46. P. K. Jain, S. Eustis, and M. A. El-Sayed, Plasmon coupling in nanorod assemblies: optical absorption, discrete dipole approximation simulation, and exciton-coupling model. The Journal of Physical Chemistry B, 2006. 110: p. 18243-18253.
47. K.-H. Su, Q.-H. Wei, X. Zhang, J. Mock, D. R. Smith, and S. Schultz, Interparticle coupling effects on plasmon resonances of nanogold particles. Nano letters, 2003. 3: p. 1087-1090.
48. S. K. Ghosh and T. Pal, Interparticle coupling effect on the surface plasmon resonance of gold nanoparticles: from theory to applications. Chemical reviews, 2007. 107: p. 4797-4862.
49. P. C. Weber, D. H. Ohlendorf, J. J. Wendoloski, and F. R. Salemme, Structural origins of high-affinity biotin binding to streptavidin. Science, 1989. 243: p. 85-88.
50. M. González, L. A. Bagatolli, I. Echabe, J. L. Arrondo, C. E. Argaraña, C. R. Cantor, and G. D. Fidelio, Interaction of biotin with streptavidin thermostability and conformational changes upon binding. Journal of Biological Chemistry, 1997. 272: p. 11288-11294.
51. M. n. González, C. E. Argaraña, and G. D. Fidelio, Extremely high thermal stability of streptavidin and avidin upon biotin binding. Biomolecular engineering, 1999. 16: p. 67-72.
52. T. Sano and C. R. Cantor, Intersubunit contacts made by tryptophan 120 with biotin are essential for both strong biotin binding and biotin-induced tighter subunit association of streptavidin. Proceedings of the National Academy of Sciences, 1995. 92: p. 3180-3184.
53. M. Howarth, D. J. Chinnapen, K. Gerrow, P. C. Dorrestein, M. R. Grandy, N. L. Kelleher, A. El-Husseini, and A. Y. Ting, A monovalent streptavidin with a single femtomolar biotin binding site. Nature methods, 2006. 3: p. 267-273.
54. M. Manning and W. Colón, Structural basis of protein kinetic stability: resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward β-sheet structure. Biochemistry, 2004. 43: p. 11248-11254.
55. K. L. Kelly, E. Coronado, L. L. Zhao, and G. C. Schatz, The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment. The Journal of Physical Chemistry B, 2003. 107: p. 668-677.