探討中性DNA與一般DNA雜交反應熱力學與結合機制之研究

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姓名

陳奕儒(Yi-Ju 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

探討中性DNA與一般DNA雜交反應熱力學與結合機制之研究
(Studies of thermodynamic and mechanism for neutralized DNA (nDNA)/DNA and DNA/DNA duplex formation)

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摘要(中)

在過去的幾十年來，由人體基因表現以作疾病的預防與臨床醫療的研究逐漸蓬勃發展，並朝向精準醫學方向邁進。而為了提升基因晶片檢測目標核酸分子雜交的效率，本研究利用一種核酸類似物，骨幹上磷酸根所帶的負電由甲基化所遮蔽，使核酸分子呈現電中性，與互補股序列DNA雜交時因為靜電排斥力的下降而有更好的穩定性，期待改質過的探針對於序列的辨識性、靈敏性、專一性得到改善。
在生物檢測平台上，感測探針性質會影響檢測之效率，因此在一股DNA當中，如何設計中性DNA核酸的最適化序列與其互補股雜交，就變成一個很重要的課題。所以此研究利用恆溫滴定微卡計(ITC)、圓二色光譜儀(CD)、熔解溫度(Tm)的量測，以熱力學和分子結構的角度探討一般DNA與中性DNA雜交之交互作用機制，再結合分子模擬來做分析，並改變不同實驗條件，包含不同鹽濃度、nDNA改質數目、序列上的修飾位置、鹼基種類等。
從CD量測的結果可以證明nDNA/DNA雜交之二級結構的形成，且與DNA/DNA形成之雙股都是B-form構型。熱力學的分析上可以發現nDNA/DNA的雜交反應是以焓為主的驅動力伴隨著大量的熵補償，並且觀察到焓熵補償效應(EEC)之現象，因此推測穩定度的貢獻主要來自於氫鍵鍵結能、鹼基堆疊和水合作用力為主，這些作用力均屬放熱反應；系統亂度包含核酸分子結構熵和水分子熵變化的總和則是下降；而不論在高、低鹽濃度下，其結合常數也大於一般DNA/DNA之雜交，說明了靜電排斥力的降低致使雜交親和力上升，從熱穩定性(Tm)也可以得到相似結果。
另外，從不同實驗條件結果可以得到一些nDNA修飾於序列的原則。nDNA改質鳥嘌呤發現Tm值上升最多，推測與鹼基體積大小，因此有不同疏水作用力有關；改質位置於序列終端會來的比序列中間穩定度提高較多，且改質nDNA的數目必須視序列長度而定，修飾越多不一定穩定度就提升，這部分可能與中性DNA甲基化產生立體障礙效應有關。初步的中性核酸分子雜交熱力學機制探討，期望提供一個最佳化序列設計，以利探針於生物檢測平台之效率提升。

摘要(英)

In the past few decades, detection and recognition of nucleic acid hybridization has been booming. In order to enhance the hybridization efficiency, we try to make a good use of neutralized DNA (nDNA) which is a DNA analogue with the backbone phosphate groups replaced by phosphate methylated groups. To reduce the electrostatic repulsion between the complementary DNA, we modified nDNA into DNA single strand and hope to improve the sensitivity and specificity of the nDNA probe. With the aim to know how the incorporation of nDNA is the optimized design, in this study we discuss a lot of different experimental conditions including nDNA numbers of modification, bases and position effect. We also proved that the nDNA sequences exhibit a stronger hybridization affinity than their corresponding DNA sequences no matter in general or the lower ionic strength buffer condition. In order to understand the hybridization thermodynamics and mechanism information from the combination of the calorimetric techniques, spectroscopic and molecular simulation were used. CD measurements highlight the modified duplexes adopt a B-form conformation that is similar to the unmodified duplexes. An entirely thermodynamic profile for nDNA/DNA hybridization suggested that nDNA-induced stability emanates from a favorable enthalpy change but a less favorable entropic term. Isothermal titration calorimetry (ITC) also showed that an increase in the binding constant between the two strands as we add nDNA while we also need to consider the DNA length. By ITC and melting studies, the modifications of nDNA in the terminal is more stable than that of in the central. And the guanine modification enhanced the thermal stability that was attributed to the stronger base stacking interaction. Our results indicated that the hybridization process of nDNA is more exothermic than the natural DNA resulting from greater hydrogen bonding especially in the lower salt concentration. We also evaluated the hybridization energies from the molecular simulation. The computed energies for the duplex involving nDNA are often larger than those for DNA/DNA due to the lower electrostatic interaction. By the experiment and simulation, we conclude the basic hybridization thermodynamic and mechanism information in order to provide a proper sequence design/modification guideline.

關鍵字(中)

★ 恆溫滴定微卡計
★ 圓二色光譜儀
★ 結合機制
★ 焓熵補償效應
★ 核酸分子

關鍵字(英)

★ isothermal titration calorimetry
★ circular dichroism
★ binding mechanism
★ enthalpy-entropy compensation
★ nucleic acid

論文目次

摘要 i
Abstract iii
誌謝 v
目錄 vii
圖目錄 x
表目錄 xiv
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 核酸結構 4
2.2 核酸類似物 5
2.2.1 肽核酸 6
2.2.2 鎖核酸 7
2.2.3 磷酸根甲基化去氧核醣核酸 9
2.3 不同系統於核酸分子雜交機制之研究 13
2.3.1 圓二色光譜儀 14
2.3.2 紫外光/可見光光譜儀 15
2.3.3 SYBR Green 18
2.3.4 分子模擬 20
2.4 單一核苷酸多形性 23
2.4.1 SNP簡介 23
2.4.2 錯誤配對辨識能力之研究 24
2.5 恆溫滴定微卡計 26
2.5.1 恆溫滴定微卡計介紹 26
2.5.2 吸附熱之計算 29
2.5.3 雜交行為之應用 30
第三章實驗藥品、儀器設備與方法 32
3.1 實驗藥品 32
3.2 儀器設備 34
3.3 實驗方法 35
3.3.1 圓二色光譜儀實驗 35
3.3.2 UV-vis分光光譜儀實驗 37
3.3.3 恆溫滴定微卡計實驗 38
3.3.4 SYBR Green螢光熔點測量儀實驗 41
3.3.5 分子模擬 43
第四章結果與討論 45
4.1 nDNA 修飾不同鹼基之探討 45
4.2 nDNA修飾不同序列位置之探討 49
4.2.1 焓熵補償效應 53
4.3 nDNA修飾數目之探討 55
4.3.1 改變鹽濃度 56
4.3.2 nDNA與LNA特性之比較 62
4.4 nDNA應用於生物檢測平台之探討 66
4.4.1 雜交熱力學之分析 66
4.4.2 FET之應用 69
4.5 nDNA辨識mismatch效果之探討 72
4.5.1 熱穩定性之分析 73
第五章結論 83
第六章參考文獻 86
附錄Appendixes 95

參考文獻

1. Dahm, R., Friedrich Miescher and the discovery of DNA. Dev Biol, 2005. 278(2): p. 274-88.
2. F.H.C., W.J.D.a.C., A Structure for Deoxyribose Nucleic Acid. Nature, 1953. 171: p. 737–738.
3. Consortium., I.H.G.S., Initial sequencing and analysis of the human genome. Nature, 2001. 409: p. 860-921.
4. Mandelkern M, E.J., Eden D, Crothers D., The Dimensions of DNA in Solution. J Mol Biol., 1981. 152: p. 153 – 61.
5. Wing R, D.H., Takano T, Broka C, Tanaka S, Itakura K, Dickerson R. , Crystal structure analysis of a complete turn of B-DNA. Nature, 1980. 287: p. 755 – 8.
6. J. Kypr, I.K., D. Renciuk and M. Vorlickova, Circular dichroism and conformational polymorphism of DNA. Nucleic acids research, 2009. 37: p. 1713-1725.
7. Leslie AG, A.S., Chandrasekaran R, Ratliff RL, Polymorphism of DNA double helices. J. Mol. Biol, 1980. 143: p. 49–72.
8. Wahl M, S.M., Crystal structures of A-DNA duplexes. Biopolymers, 1997. 44: p. 45 – 63.
9. Lu XJ, S.Z., Olson WK, A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol., 2000. 300: p. 819–40.
10. Takayuki Natsumea, Yasuyuki Ishikawab, Kenichi Dedachia, Takayuki Tsukamotoa, Noriyuki Kurita, Hybridization energies of double strands composed of DNA, RNA, PNA and LNA. Chem Phys Lett, 2007. 434(1-3): p. 133-138.
11. Tommi Ratilainen, A.H. and E.T. ´n, Peter E. Nielsen, and Bengt Norde, Thermodynamics of Sequence-Specific Binding of PNA to DNA. Biochemistry, 2000. 39: p. 7781-7791.
12. MICHAEL EGHOLM, O.B., LEIF CHRISTENSEN, CARSTEN BEHREN, SUSAN M. FREIER, DAVID A. DRIVER, ROLF H. BERG, SEOG K. KIM, BENGT NORDEN & PETER E. NIELSEN, PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules. Nature, 1993. 365: p. 566 - 568.
13. Sebastian Tomac , M.S., Tommi Ratilainen ,Pernilla Wittung , Peter E. Nielsen , Bengt Nordén , and Astrid Gräslund, Ionic Effects on the Stability and Conformation of Peptide Nucleic Acid Complexes. J. Am. Chem. Soc, 1996. 118: p. 5544–5552.
14. Nielsen, M.E.P.E., Solution structure of a peptide nucleic acid DNA duplex. Nature Structural Biology, 1996. 3(410-413).
15. MICHAEL EGHOLM, OLE BUCHARDT, LEIF CHRISTENSEN, CARSTEN BEHRENS, SUSAN M. FREIER, DAVID A. DRIVER, ROLF H. BERG, SEOG K. KIM, BENGT NORDEN & PETER E. NIELSEN, PNA hybridizes to complementary oligonucleotides obeying the Watson Crick hydrogen-bonding rules. 1993
16. Nielsen, P.E., Peptide nucleic acids as therapeutic agents. Current Opinion in Structural Biology, 1999. 9(3): p. 353-357.
17. Satoshi Obikaa, Daishu Nanbua, Yoshiyuki Haria, Ken-ichiro Morioa, Yasuko Inb, Toshimasa Ishidab, Takeshi Imanishi, Synthesis of 2′-O, 4′-C-methyleneuridine and-cytidine. Novel bicyclic nucleosides having a fixed C 3,-endo sugar puckering. Tetrahedron Letters, 1997. 38(50): p. 8735-8738.
18. Singh, S.K., Nielsen, P., Koshkin, A., and Wengel, J., LNA(locked nucleic acids): Synthesis and high-affinity nucleic acid recognition. Chem. Commun, 1998: p. 455-456.
19. Wengel, J., Petersen, M., Nielsen, K. E., Jensen, G. A., Håkansson,, K. A. E., R., Sorensen, M. D., Rajwanshi, V. K., Bryld, T.,, and J.P. and Jacobsen, LNA (locked nucleic acid) and the diastereoisomeric R-L-LNA: Conformational tuning and high affinity of DNA/RNA targets. Nucleosides, Nucleotides Nucleic Acids, 2001. 20: p. 389-396.
20. Kaur, H., J. Wengel, and S. Maiti, Thermodynamics of DNA-RNA heteroduplex formation: effects of locked nucleic acid nucleotides incorporated into the DNA strand. Biochemistry, 2008. 47(4): p. 1218-27.
21. Petersen M, W.J., LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol, 2003. 21: p. 74-81.
22. Kareem Fakhfakh,Olivia Marais,Xin Bo Justin Cheng,Jorge Real Castañeda,
Curtis B. Hughesman,Charles Haynes, Molecular thermodynamics of LNA:LNA base pairs and the hyperstabilizing effect of 5′-proximal LNA:DNA base pairs. AIChE Journal, 2015. 61(9): p. 2711-2731.
23. Jakobsen MR, H.J., Wengel J, Berkhout B, Kjems J., Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites. Retrovirology, 2007. 4(29).
24. Wahlestedt C, S.P., Good L, et al., Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc Natl Acad Sci USA, 2000. 97(10): p. 5633–5638.
25. Karlsen KK, W.J., Locked nucleic acid and aptamers. Nucleic Acid Ther, 2012. 22(6): p. 366-370.
26. Barciszewski J, M.M., Koch T, Kurreck J, Erdmann VA, Locked nucleic acid aptamers. Methods Mol Biol, 2009. 535: p. 165-186.
27. Mallikaratchy PR, R.A., Gardner JR, et al, A multivalent DNA aptamer specific for the B-cell receptor on human lymphoma and leukemia. Nucleic Acids Res, 2011. 39(6): p. 2458–2469.
28. Ugozzoli LA, L.D., Puckett R, Arar K, Hamby K, Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Anal Biochem, 2004. 324(1): p. 143-152.
29. Warshawsky I, M.F., Locked nucleic acid probes for enhanced detection of FLT3 D835/I836, JAK2 V617F and NPM1 mutations. J Clin Pathol, 2011. 64(10): p. 905-910.
30. Leo H. Koole, Harold M. Moody, Niek L. H. L. Broeders, Peter J. L. M.Quaedflieg, Will H. A. Kuijpers, Marcel H. P. Van Genderen, Annie J. J. M. Coenen, Sjoerd Van der Wal, Henk M. Buck, Synthesis of hosphate-methylated DNA fragments using 9-fluorenylmethoxycarbonyl as transient base protecting group. . The Journal of Organic Chemistry, 1989. 54(7): p. 1657-1664.
31. W.H.A. Kuijpers, J. Huskens, L.H. Koole and C.A.A. van Boeckel, Synthesis of well-defined phosphate-methylated DNA fragments: the application of potassium carbonate in methanol as deprotecting reagent. Nucleic acids research, 1990. 18(17): p. 5197-5205.
32. van Genderen, M.H., L.H. Koole, and H.M. Buck, Hybridization of phosphate‐methylated DNA and natural oligonucleotides. Implications for protein‐induced DNA duplex destabilization. Recueil des Travaux Chimiques des Pays-Bas, 1989. 108(1): p. 28-35.
33. Miller PS, Fang KN, Kondo NS, Ts′o PO, Syntheses and properties of adenine and thymine nucleoside alkyl phosphotriesters, the neutral analogs of dinucleoside monophosphates. Journal of the American Chemical Society, 1971. 93(24): p. 6657.
34. Miller, P.S., L.T. Braiterman, and P.O. Ts′o, Effects of a trinucleotide ethyl phosphotriester, Gmp (Et) Gmp (Et) U, on mammalian cells in culture. Biochemistry. Biochemistry, 1977. 16(9): p. 1988-1996.
35. Koole, L.H.a.H.M.B., Enhanced stability of a Watson & Crick DNA duplex structure by methylation of the phosphate groups in one strand. in Proc. K. Ned. Acad. Wet, 1987.
36. Kankia, B.I., Kupke, D. W., and Marky, L. A, The Incorporation of a Platinated Cross-Link into Duplex DNA Yields an Uptake of Structural Water. J. Am. Chem. B, 2001. 105: p. 11402-11405
37. Biman Jana, S.P., Prabal K. Maiti, Shiang-Tai Lin, James T. Hynes, and and B. Bagchi, Entropy of Water in the Hydration Layer of Major and Minor Grooves of DNA. J. Phys. Chem. B, 2006. 110: p. 19611-19618.
38. Zewail, S.K.P.a.A.H., Dynamics of Water in Biological Recognition. Chem. Rev, 2004. 104(4): p. 2099–2124.
39. Bhattacharyya, K., Solvation Dynamics and Proton Transfer in Supramolecular Assemblies. Acc. Chem. Res, 2003. 36(2): p. 95-101.
40. Otting, G., NMR studies of water bound to biological molecules. Progress in Nuclear Magnetic Resonance Spectroscopy, 1997. 31(2-3): p. 259-285.
41. Lin, F.Y., Chen, W. Y., Hearn, M. T. W, Microcalorimetric Studies on the Interaction Mechanism Between Proteins and Hydrophobic Solid Surfaces in Hydrophobic Interaction Chromatography : Effects of Salts, Hydrophobicity of the Sorbent, and Structure of the Protein. Anal.Chem, 2001. 73: p. 3875.
42. Florian, J., Sponer, J., and Warshel, A, Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study. J. Phys. Chem, 1999. 103: p. 884-892.
43. Soto, A.M., Kankia, B. I., Dande, P., Gold B., and Marky, L. A, Thermodynamic and Hydration Effects for the Incorporation of a Cationic 3-Aminipropyl Chain into DNA. Nucleic Acids Research, 2002. 30: p. 3171-3180.
44. Gromiha, P.K.P.a.M.M., On the Conformational Stability of Oligonucleotide Duplexes and tRNA Molecules. J.theor. Biol, 1994. 169: p. 419-432.
45. Siligardi, Giuliano; Hussain, Rohanah; Berova, Nina; Vorlíčková, Michaela; Kejnovská, Iva; Bednářová, Klára; Renčiuk, Daniel; Kypr, Jaroslav, Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes. Chirality, 2012. 24(9): p. 691-698.
46. Gray DM, R.R., Vaughan MR, Circular dichroism spectroscopy of DNA. Methods Enzymol 1992. 211: p. 389-406.
47. Johnson WC, J., Determination of the conformation of nucleic acids by electronic CD. In: Fasman GD, editor. Circular dichroism and the conformational analysis of biomolecules. New York: Plenum press, 2000: p. 433-468.
48. Jaroslav Kypr, Iva Kejnovská, Daniel Renčiuk and Michaela Vorlíčková, Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res, 2009. 37(6): p. 1713-25.
49. Peng Wu, S.-i.N.a.N.S., Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur. J. Biochem, 2002. 269: p. 2821–2830.
50. Jens Kurreck, E.W., Clemens Gillen, and Volker A. Erdmann, Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Research, 2002. 30(9): p. 1911-1918.
51. Maiti, N.K.a.S., Role of Locked Nucleic Acid Modified Complementary Strand in Quadruplex/Watson-Crick Duplex Equilibrium. J. Phys. Chem. B, 2007. 111: p. 12328-12337.
52. Gilles Bruylants, Marina Boccongelli, Karim Snoussi and Kristin Bartik, Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex. Biochemistry, 2009. 48(35): p. 8473-82.
53. Naoki Sugimoto, S.-i.N., Misa Katoh, Akiko Matsumura, Hiroyuki Nakamuta, Tatsuo Ohmichi,Mari Yoneyama, and Muneo Sasaki, Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes. Biochemistry, 1995: p. 11211-11216.
54. Koshkin, A.A., Nielsen, P., Meldgaard, M., Rajwanshi, V. K., Singh, S. K., and Wengel, J, LNA (locked nucleic acid): an RNA mimic forming exceedingly stable LNA:LNA duplexes. J. Am. Chem. Soc, 1998. 120: p. 13252–13253.
55. Patricia M. McTigue, Raymond J. Peterson,, and Jason D. Kahn, Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)-DNA Duplex Formation. Biochemistry, 2004. 43: p. 5388-5405.
56. Elzbieta Kierzek, Anna Pasternak, Karol Pasternak, Zofia Gdaniec, Ilyas Yildirim, Douglas H. Turner and Ryszard Kierzek, Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2′-O-methyl RNA with locked nucleic acids. Biochemistry, 2009. 48(20): p. 4377-87.
57. Hubert Zipper, Herwig Brunner, Jürgen Bernhagen and Frank Vitzthum, Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res, 2004. 32(12): p. e103.
58. E.Navarro, G.S.H., M.J. Castano, J. Solera Real-time PCR detection chemistry. Clinica Chimica Acta, 2015. 439(15): p. 231-250.
59. Ian M. Mackay, K.E.A.a.A.N., Real-time PCR in virology. Nucleic Acids Research, 2002. 30(6): p. 1292-1305.
60. Harris, S.A., Z.A. Sands, and C.A. Laughton, Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA. Biophys J, 2005. 88(3): p. 1684-91.
61. Mark Stoneking, H.G., Single nucleotide polymorphisms From the evolutionary past. Nature, 2001. 409: p. 821-822.
62. Chakravarti, A., Single nucleotide polymorphisms: to a future of genetic medicine. Nature, 2001. 409: p. 822-823.
63. Chou, L.-S., Meadows,C., Wittwer,C.T. and Lyon,E, Unlabeled oligonucleotide probes modified with locked nucleic acids for improved mismatch discrimination in genotyping by melting analysis. BioTechniques, 2005. 39: p. 644-647.
64. Kauppinen, S., Nielsen,P.S., Mouritzen,P., Nielsen,A.T., Vissing,H.,Møller,S. and Ramsing,N.B, LNA microarrays in genomics. PharmaGenomics. 3: p. 24-34.
65. Du, H., Strohsahl,C.M., Camera,J., Miller,B.L. and Krauss,T.D. , Sensitivity and specificity of metal surface-immobilized ‘molecular beacon’ biosensors. J. Am. Chem. B, 2005. 127: p. 7932–7940.
66. Yong You, Bernardo G. Moreira, Mark A. Behlke and Richard Owczarzy, Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res, 2006. 34(8): p. e60.
67. Doench, J.G.S., P. A, Specificity of microRNA Target Selection in Translational Repression. Genes Dev, 2004. 18: p. 504-511.
68. Clanton-Arrowood, K.M., J.; Schroeder, S. J, Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices. Biochemistry, 2008. 47: p. 13418-13427.
69. Ohmichi, T.N., S.; Miyoshi, D.; Sugimoto, N. Long, Dangling End Has Large Energetic Contribution to Duplex Stability. J. Am. Chem. Soc, 2002. 124: p. 10367-10372.
70. Jhimli Bhattacharyya, Souvik Maiti, Sanjukta Muhuri, Shu-ichi Nakano, Daisuke Miyoshi, and Naoki Sugimoto. Effect of locked nucleic acid modifications on the thermal stability of noncanonical DNA structure. Biochemistry, 2011. 50(34): p. 7414-25.
71. Haibo Liu, J.G., Stephen R. Lynch, Y. David Saito, Lystranne Maynard, Eric T. Kool, A Four–Base Paired Genetic Helix with Expanded Size. SCIENCE, 2003. 302: p. 868-871.
72. Salvatore Bommarito, N.P.a.J.S.J., Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Research, 2000. 28(9): p. 1929-1934.
73. David H. Mathews, J.S., Michael Zuker and Douglas H. Turner, Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure. J. Mol. Biol, 1999. 288: p. 911-940.
74. Gilbert S. D., S.C.D., Wise S. J., and Batey R. T., Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol, 2006. 359: p. 754-768.
75. Bishop G. R., R.J.S., Polander B. C., Jeanfreau B. D., Trent J. O., and Chaires J. B., Energetic basis of molecular recognition in a DNA aptamer. Biophysical Chemistry, 2007. 126: p. 165-175.
76. Krzysztof Ziomek, E.K., Ewa Biala, Ryszard Kierzek, The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides. Biophysical Chemistry 97, 2002: p. 233–241.
77. Paola Gilli, V.F., Gastone Gilli, Pier Andrea Borea, Enthalpy-entropy compensation in drug-receptor binding. J. Phys. Chem, 1994. 98(5): p. 1515–1518.
78. McPhail, D.C., A, Thermodynamics and kinetics of dissociation of ligand-induced dimers of vancomycin anti-biotics. J. Chem. Soc, 1997. 93: p. 2283-2289.
79. Allawi, H.S., J. Jr Thermodynamics andNMR of internal GÆT mismatches in DNA. Biochemistry, 1997. 36: p. 10581–10594
80. Wu, P., S.-i. Nakano, and N. Sugimoto, Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. European Journal of Biochemistry, 2002. 269(12): p. 2821-2830.
81. Harleen Kaur, A.A., Jesper Wengel,and Souvik Maiti, Thermodynamic, Counterion, and Hydration Effects for the Incorporation of Locked Nucleic Acid Nucleotides into DNA Duplexes. Biochemistry, 2006. 45: p. 7347-7355.
82. P.H. Lin, R.H.C., C.H. Lee, Y. Chang, C.S. Chen and W.Y. Chen, Studies of the binding mechanism between aptamers and thrombin by circular dichroism, surface plasmon resonance and isothermal titration calorimetry. Colloids and surfaces. B, Biointerfaces, 2011. 88: p. 552-558.
83. Kuo-Chih Lin, Ming-Tsai Wey, Lou-Sing Kan, David Shiuan, Characterization of the Interactions of Lysozyme with DNA by Surface Plasmon Resonance and Circular Dichroism Spectroscopy. Applied Biochemistry and Biotechnology, 2009. 158(3): p. 631-641.
84. Genderen, v.M., Structure and stability of phosphate-methylated DNA duplexes: model systems for specific DNA-protein interaction and conformational transmission. Technische Universiteit Eindhoven, 1989.
85. J Petruska, M.F.G., M S Boosalis, L C Sowers, C Cheong, and I Tinoco, Jr, Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc Natl Acad Sci USA, 1988. 85(17): p. 6252–6256.
86. Leal, C., Wadso, L., Olofsson, G., Miguel, M., and Wennerstrom, H, DNA and DNA-Surfactant Hydration. 2002.
87. Luye Mu, Y.C., Sonya D. Sawtelle, Mathias Wipf, and Xuexin Duan Silicon Nanowire Field-Effect Transistors - A Versatile Class of Potentiometric Nanobiosensors. IEEE Access, 2015. 3.
88. Chi-Chang Wu, T.-M.P., Chung-Shu Wu, Li-Chen Yen, Cheng-Keng Chuang, See-Tong Pang, Yuh-Shyong Yang, Fu-Hsiang Ko Label-free Detection of Prostate Specific Antigen Using a Silicon Nanobelt Field-effect Transistor. Int. J. Electrochem. Sci., 2012. 7: p. 4432-4442.
89. Zhiqiang Gao, A.A., Alastair D. Trigg, Navab Singh, Cheng Fang, Chih-Hang Tung, Yi Fan, Kavitha D. Buddharaju, and Jinming Kong Silicon nanowire arrays for label-free detection of DNA. Anal. Chem, 2007. 79(9): p. 3291-3297.
90. Seong-Wan Ryua, C.-H.K., Jin-Woo Hana, Chung-Jin Kima, Cheulhee Jungb, Hyun Gyu Parkb, Yang-Kyu Choi Gold nanoparticle embedded silicon nanowire biosensor for applications of label-free DNA detection. Biosensors Bioelectron, 2010. 25(9): p. 2182-2185.
91. E. Stern, R.W., F. J. Sigworth, R. Breaker, T. M. Fahmy, and M. A. Reed Importance of the Debye screening length on nanowire field effect transistor sensors. Nano Lett, 2007. 7(11): p. 3405-3409.
92. Chris M. Olsen, H.-T.L., and Luis A. Marky, Unfolding Thermodynamics of Intramolecular G-Quadruplexes: Base Sequence Contributions of the Loops. J. Phys. Chem. B, 2009. 113: p. 2587-2595.
93. Cosimo Antonacci, J.B.C., and Richard D. Sheardy, Biophysical Characterization of the Human Telomeric (TTAGGG)4 Repeat in a Potassium Solution. Biochemistry, 2007. 46: p. 4654-4660.
94. Mouritzen, P., Nielsen,A.T., Pfundheller,H.M., Choleva,Y.,Kongsbak,L. and Møller,S, Single nucleotide polymorphismgenotyping using locked nucleic acid (LNA). Expert Rev. Mol.Diagn, 2003. 3: p. 27-38.
95. Marta Hernandez, D.R.-L., Teresa Esteve, Salome Prat, and Maria Plaa, Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection. Analytical Biochemistry, 2003. 323: p. 164-170.
96. K.M. Ririe, R.P.R., C.T. Wittwer Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem, 1997. 245: p. 154-160.
97. Ana Maria Soto, B.I.K., Prasad Dande,Barry Gold and Luis A. Marky Thermodynamic and hydration effects for the incorporation of a cationic 3‐aminopropyl chain into DNA. Nucleic Acids Res, 2002. 30(14): p. 3171-3180.
98. Kool, B.A.S.a.E.T., Hydrophobic,Non-Hydrogen-Bonding Bases and Base Pairs in DNA. American Chemical Society, 1995. 117(7).
99. Richard Owczarzy, Yong You, Christopher L. Groth, and Andrey V. Tataurov, Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry, 2011. 50(43): p. 9352-67.
100. Ladbury, J.E., Application of isothermal titration calorirnetry in the biological sciences:Things are heating up! Biotechniques, 2004. 37: p. 885-887.

指導教授

陳文逸(Wen-Yih Chen)

審核日期

2016-7-22

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