請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/47722
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 李雨 | |
dc.contributor.author | Rui-Bin Jiang | en |
dc.contributor.author | 江瑞斌 | zh_TW |
dc.date.accessioned | 2021-06-15T06:14:43Z | - |
dc.date.available | 2010-08-18 | |
dc.date.copyright | 2010-08-18 | |
dc.date.issued | 2010 | |
dc.date.submitted | 2010-08-11 | |
dc.identifier.citation | 1. Albarran, B., To, R., Stayton, P. S. (2005) 'A TAT-streptavidin fusion protein directs uptake of biotinylated cargo into mammalian cells'. Protein Engineering, Design and Selection 18: 147-152.
2. Anderson, K., Areskong, D., Hardenborg, E. (1999) 'Exploring buffer space for molecular interactions. Journal of Molecular Recognition 12: 310-315. 3. Asanov, A. N., Wilson, W. W., Oldham, P. B. (1998) 'Regenerable biosensor platform: a total internal reflection fluorescence cell with electrochemical control'. Analytical Chemistry 70: 1156-1163. 4. Bagotsky, V. S. (2006) 'Fundamentals of Electrochemistry'. John Willey & Sons, Inc., New Jersey. 5. Bearinger, J. P., Voros, J., Hubbell, J. A., Textor, M. (2003) 'Electrochemical optical waveguide lightmode spectroscopy (EC-OWLS): a pilot study using evanescent-field optical sensing under voltage control to monitor polycationic polymer adsorption onto Indium Tin Oxide (ITO)-coated waveguide chips'. Biotechnology and Bioengineering 82: 465-473. 6. Bell, G. I. (1978) 'Models for the specific adhesion of cells to cells'. Science 200: 618-627. 7. Berezhinsky, L. I., Chegel, V. I., Shirshov, Y. M. (2001) 'SPR- spectroscopy of protein molecules adsorbed in microwave field'. Semiconductor Physics, Quantum Electronics and Optoelectronics. 4: 343-346. 8. Bingham, J. P., Bian, S., Tan, Z. Y., Takacs, Z., Moczydlowski, E. (2006) 'Synthesis of a biotin derivative of Iberiotoxin: binding interactions with streptavidin and the BK Ca2+-activated K+ channel expressed in a human cell line'. Bioconjugate Chemistry 17: 689-699. 9. Bos, M. A., Shervani, Z., Anusiem, A. C. I., Giesbers, M., Norde, W., Kleijn, J. M. (1994) 'Influence of the electric potential of the interface on the adsorption of proteins'. Colloids and Surfaces B 3: 91-100. 10. Brusatori, M. A., Van Tassel, P. R. (2003) 'Biosensing under an applied voltage using optical waveguide lightmode spectroscopy'. Biosensors and Bioelectronics 18: 1269-1277. 11. Chaiet, L., Wolf, F. J. (1964) 'The properties of streptavidin, a biotin-binding protein produced by streptomycetes'. Archives of Biochemistry and Biophysics 106: 1-5. 12. Chang, R. (1991) 'Chemistry'. McGraw-Hill, Inc., New Jersey. 13. Chatelier, R. C. (1995) 'A general method to recondition and reuse BIAcore sensor chips fouled with covalently immobilized protein/peptide'. Analytical Biochemistry 229: 112-118. 14. Chen, S., Springer, T. A. (2001) 'Selection receptor-ligand bonds: formation limited by shear rate and dissociation governed by the Bell model'. Proceedings of the National Academy of Sciences 98: 950-955. 15. Darst, S. A., Ahlers, M., Meller, P. H., Kubalek, E. W., Blankenburg, R., Ribi, H. O., Ringsdorf, H., Kornberg, R. D. (1991) 'Two-dimensional crystals of streptavidin on biotinylated lipid layers and their Interactions with biotinylated macromolecules'. Biophysical Journal 59: 387-396. 16. Derenyi, I., Bartolo, D., Ajdari, A. (2003) 'Effects of intermediate bond states in dymamics force spectroscopy'. Analytical Biochemistry 312: 175-181. 17. Eberbeck, D., Bergemann, C., Weikhorst, F., Steinhoff, U., Trahms, L. (2008) 'Quantification of specific bindings of biomolecules by magnetorelaxometry'. Journal of Nanobiotechnology 6: 1-12. 18. Elimelech, M., Gregory, J., Jian, X., Williams, R. A. (1995) 'Particle Deposition and Aggregation'. Butterworth-Heinemann Ltd., Boston. 19. Enikov, E. T., Seo, G. S., Kuwahara, S., Miller, T., Palaria, A., Cuello, J. L. (2006) 'AFM study of field-assisted adsorption of proteins and particles on inorganic surfaces'. Unpublished. 20. Ermak, D. L., McCammon, J. A. (1978) 'Brownian dynamics with hydrodynamic interactions'. Journal of Chemical Physics 69: 1352-1360. 21. Evans, E. (2001) 'Probing the relation between force lifetime and chemistry in single molecular bonds'. Annual Review of Biophysics and Biomolecular Structure 30: 105-128. 22. Evans, E. (1998) 'Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy'. Faraday Discuss 111: 1-16. 23. Evans, E., Ritchie, K. (1997) 'Dynamic strength of molecular adhesion bonds'. Biophysical Journal 72: 1541-1555. 24. Farkas, L. (1927) 'Keimbildungsgeschwindigkeit in ubersattigen dampfen'. Zeitschrift fur Physikalische Chemie 125: 236-242. 25. G-Biosciences Technical (2010) 'HOOK(TM)-Biotin Labeling Handbook'. G-Biosciences Technical. 26. Gardiner, C. W. (1985) 'Handbook of Stochatic Methods'. Springer. New York. 27. Gooding, J. J., Wasiowych, C., Barnett, D., Hibbert, D. B., Barisci, J. N., Wallace, G. G. (2004) 'Electrochemical modulation of antigen-antibody binding'. Biosensors and Bioelectronics 20: 260-268. 28. Green, M. (1975) 'Avidin'. Advances in Protein Chemistry 29: 85-133. 29. Grubmuller, H., Heymann, B., Tavan, P. (1996) 'Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force'. Science 271: 997-999. 30. Hanggi, P., Talkner, P., Borkovec, M. (1990) 'Reaction rate theory: fifty years after Kramers'. Reviews of Modern Physics 62: 251-342. 31. Howard, J. (2001) 'Mechanics of Motor Proteins and the Cytoskeleton'. Sinauer Associates, Inc., Massachusetts. 32. Howarth, M., Chinnapen, D. J. F., Gerrow, K., Dorrestein, P. C., Grandy, M. R., Kelleher, N. L., El-Husseini, A., Ting, A. Y. (2006) 'A monovalent streptavidin with a single femtomolar biotin binding site'. Nature Methods 3: 267-273. 33. Huber, G. A., Kim, S. (1996) 'Weighted ensemble Brownian dynamics simulations for protein association reactions'. Biophysical Journal 70: 97-110. 34. Hwang, R. Z., Huang, L. S., Chang, H. S., Wu, C. W., Tien, H. C., Lin, S., Lee, A. S. Y. (2005) 'A novel reusable nanomechanics-based protein biosensor with electrical manipulation'. 18th IEEE International Conference on Micro Electro Mechanical System. 35. Hyre, D. E., Trong, I. L., Merritt, E. A., Ecclestion, J. F., Green, N. M., Stenkamp, R. E., Stayton, P. S. (2006) 'Cooperative hydrogen bond interactions in the streptavidin-biotin system'. Protein Science 15: 459-467. 36. Israelachivili, J. N. (1992) 'Intermolecular and Surface Forces'. Academic Press Inc., London. 37. Karnik, R., Duan, C., Castelino, K., Daijuji, H., Majumdar, A. (2007) 'Rectification of ionic current in a nanofluidic diode'. Nano Letters 7: 547-551. 38. Kozack, R. E., d'Mello, M. J., Subramaniam, S. (1995) 'Computer modeling of electrostatic steering and orientational effects in antibody-antigen association'. Biophysical Journal 68: 807-814. 39. Kudo, Y., Kusabiraki, M. (2006) 'Oxygen-plasma treatment of Indium Tin Oxide in a triode glow discharge'. Japanese Journal of Applied Physics 45: 8517-8520. 40. Lamm, G., Schulten, K. (1982) 'Extended Brownian dynamics. II. Reactive, nonlinear diffusion'. Journal of Chemical Physics 78: 2713-2734. 41. Leckband, D., Israelachvili, J. N. (2001) 'Intermolecular Forces in Biology'. Quarterly Reviews of Biophysics 34: 105-267. 42. Lee, J. O., So, H. M., Jeon, E. K., Chang, H., Won, K., Kim, Y. H. (2008) 'Aptamers as molecular recognition elements for electrical nanobiosensors'. Analytical and Bioanalytical Chemistry 390: 1023-1032. 43. Liron, Z., Tender, L. M., Golden, J. P., Ligler, F. S. (2002) 'Voltage-induced inhibition of antigen-antibody binding at conducting optical waveguides'. Biosensors and Bioelectronics 17: 489-494. 44. Livnah, O., Bayer, E. A., wilchek, M., Sussman, J. L. (1993) 'Three-dimensional structures of avidin and the avidin-biotin complex'. Proceedings of the National Academy of Sciences 90: 5076-5080. 45. No, D. (2008) 'Localized surface plasmon resonance nanobiosensors for the detection of a prostate cancer biomarker'. Nanoscape 5: 15-19. 46. Northrup, S. H., Allison, S. A., McCammon, J. A. (1984) 'Brownian dynamics simulation of diffusion influenced bimolecular reactions'. J. Chem. Phys. 80: 1517-1524. 47. Ohshima, H. (1998) 'Electrical Phenomena at Interfaces'. Marcel Dekker, Inc., New York. 48. Ooya, T., Yui, N. (2002) 'Multivalent interactions between biotin-polyrotaxane conjugates and streptavidin as a model of new targeting for transporters'. Journal of Controlled Release 80: 219-228. 49. Piran, U., Riordan, W. J. (1990) 'Dissociation rate constant of the biotin-streptavidin complex'. Journal of Immunological Methods 133: 141-143. 50. Prez-Luna, V. H., O'Brien, M. J., Opperman, K. A., Hampton, P. D., Lpez,G. P., Stayton, P. S. (2010) 'Molecular recognition between genetically engineered streptavidin and surface-bound biotin'. Journal of the American Chemical Society 121: 6469-6478. 51. Qureshi, M. H., Wong, S. L. (2002) 'Design, production, and characterization of a monomeric streptavidin and its application for affinity purification of biotinylated proteins'. Protein Expression and Purification 25: 409-415. 52. Qureshi, M. H., Yeung, J. C., We, S. C., Wong, S. L. (2001) 'Development and characterization of a series of soluble tetrameric and monomeric streptavidin muteins with differential biotin binding affinities'. Journal of Biological Chemsitry 276: 46422-46428. 53. Rahman, A. (1964) 'Correlations in the motion of atoms in liquid argon'. Physical Review 135: A405-A411. 54. Raschke, G., Kowarik, S., Franzl, T., Sonnichsen, C., Klar, T. A., Feldmann, J. (2003) 'Biomolecular recognition based on single gold nanoparticle light scattering'. Nano Letters 3: 935-938. 55. Sano, T., Cantor, C. R. (1995) 'Intersubunit contacts made by Tryptophan 120 with biotin are essential for both strong biotin binding and biotin-induced tighter subunit asociation of streptavidin'. Proceedings of the National Academy of Sciences 92: 3180-3184. 56. Schwartz, J. J., Quake, S. R. (2007) 'High density single molecule surface patterning with colloidal epitaxy'. Applied Physics Letters 91: 083902. 57. Schwidop, W. D. (1990) 'Procedure for The purification of streptavidin by hydrophobic interaction chromatography'. Journal of Chromatography 520: 325-331. 58. Smith, E. B. (2004) 'Basic Chemical Thermodynamics'. Imperial College Press, London. 59. Srisa-Art, M., Dyson, E. C., deMello, A. J., Edel, J. B. (2008) 'Monitoring of real-time streptavidin-biotin binding kinetics using droplet microfluidics'. Analytical Chemistry 80: 7063-7067. 60. Strandh, M. (2000) 'Insights into weak affinity antibody-antigen interactions. Doctorial dissertation'. University of Kalmar. 61. Tang, T., Hui, C. Y., Jagota, A. (2006) 'Adhesive contact driven by electrostatic forces. Journal of Applied Physics. 99: 054906. 62. Valimaa, L. 'Streptavidin: a versatile binding protein for solid-phase immunoassays'. Doctorial dissertation. University of Turku . 2008. 63. Zhang, J., Drechsler, A., Grundke, K., Kwok, D. Y. (2004) 'A simple and practical approach to implement the general Poisson-Boltzmann equation of symmetric and asymmetric electrolytes for electrical double layer interactions'. Colloids and Surfaces A 242: 189-193. 64. Zourob, M., Mohr, S., Brown, B. J. T., Fielden, P. R., McDonneell, M. B., Goddardb, N. J. (2005) 'An integrated optical leaky waveguide sensor with electrically induced concentration system for the detection of bacteria'. Lab on a Chip 5: 1360-1365. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/47722 | - |
dc.description.abstract | The literature showed that the immune type biosensors can be regenerated by applying a voltage of order of one volt across the combined macromolecules, but the underlying physics was not clarified. Such a method for regeneration via physical means is of particular interest for developing possible implantable biosensor where the conventional regeneration via chemical elution is unavailable. Thus the goal of this dissertation is to carry out a rigorous study for understanding the physics behind the regeneration, and a detailed parametric study which is helpful for designing effective re-generable biosensor using substrate electric potential.
By incorporating an electric double layer force and a van der Waals force into a weight-ensemble Brownian dynamics simulation under a prescribed molecular interaction force between specific interacting macromolecules, we found that the dissociation rate constant for biotin-streptavidin increases exponentially with , and reaches more than 400 folds when equals one volt. The results are qualitatively similar using either the result from molecular dynamic simulation or the Lennard-Jones model for the prescribed interaction force between biotin and streptavidin. Examination of detailed forces shows that it is the electric double layer force that lowers the energy barrier mainly set by the molecular interaction force associated with the specific interacting molecules, so that the random thermal force has more chance to tear those associated macromolecules apart. With the enhanced dissociation rate constant obtained, a series of macroscopic diffusion simulation was performed with the aid of the commercial software, COSMOL. The result agrees fairly well with the previous experiment for the entire association-dissociation process. Also the calculations with the enhanced dissociation rate constants explain quantitatively the experimental finding that the regeneration using square-wave voltage is superior to that using saw-tooth voltage. This is because that the dissociation rate constant increases exponentially with the applied voltage, and the associated complex is exposed to larger applied voltage (and thus much larger dissociation rate constant) over a longer time duration for the square-wave voltage manipulation. Parametric studies were performed including effects of different applied signals, different surrounding temperature, and different linker lengths. It is found that the regeneration is enhanced as the applied voltage increases, as the temperature increases, and as the linker length decreases. | en |
dc.description.provenance | Made available in DSpace on 2021-06-15T06:14:43Z (GMT). No. of bitstreams: 1 ntu-99-D93543011-1.pdf: 1455896 bytes, checksum: a46da9c6596facb11deb5012a2eebafc (MD5) Previous issue date: 2010 | en |
dc.description.tableofcontents | Acknowledgement i
Abstract ii 摘要 iv Chapter 1 Introduction 1 1.1 Biosensor 1 1.1.1 Typical non-covalent specific biomolecular interactions 2 1.1.2 Representative methods for the estimation of interaction kinetics 4 1.2 Regeneration 9 1.3 Experiments about physical regeneration 12 1.4 Statements of purpose 13 Chapter 2 Theory 15 2.1 Introduction 15 2.2 Reaction rate 16 2.2.1 Rate of chemical reaction 17 2.2.2 Kinetics 17 2.2.3 Rate theory 21 2.3 Review of intermolecular and surface forces 29 2.4 Theory and numerical method for the biosensor regeneration via substrate electric potential 39 2.4.1 Introduction 39 2.4.2 COSMOL software 40 2.4.3 Weighted ensemble Brownian dynamics simulation 42 2.3.4 Intermolecular interactions in calculation 49 2.3.4.1 van der Waals force 51 2.3.4.2 Electrostatic force 51 Chapter 3 Results 61 3.1 Deterministic forces 61 3.2 Dissociation rate constants 62 3.3 Concentration curves 65 3.4 Comparison between the saw-tooth and square-wave voltage manipulation…. 68 3.5 Using Lennard-Jones model for molecular interaction force 69 3.6 Temperature effect 73 3.7 Dissociation enhancement under constant force 73 3.8 Effect of linker length 75 Chapter 4 Conclusions 77 References 80 Figures 91 Tables 118 | |
dc.language.iso | en | |
dc.title | 以基板電壓作生醫感測晶片再生的物理機制及參數研究 | zh_TW |
dc.title | Physical Mechanism and Parametric Study of Biosensor Regeneration via Substrate Electric Potential | en |
dc.type | Thesis | |
dc.date.schoolyear | 98-2 | |
dc.description.degree | 博士 | |
dc.contributor.oralexamcommittee | 吳光鐘,張正憲,趙聖德,陳俊杉 | |
dc.subject.keyword | 生醫晶片,晶片再生,基材電壓,專一性作用,分子間作用力,加權樣本布朗動力計算, | zh_TW |
dc.subject.keyword | biosensor,regeneration,substrate electric potential,specific interaction,intermolecular forces,weight-ensemble Brownian dynamics simulation, | en |
dc.relation.page | 122 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2010-08-12 | |
dc.contributor.author-college | 工學院 | zh_TW |
dc.contributor.author-dept | 應用力學研究所 | zh_TW |
顯示於系所單位: | 應用力學研究所 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-99-1.pdf 目前未授權公開取用 | 1.42 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。