博碩士論文 952411002 詳細資訊




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姓名 林伯勳(Po-Hsun Lin)  查詢紙本館藏   畢業系所 系統生物與生物資訊研究所
論文名稱 利用恆溫滴定微卡計,圓二色光譜儀和分子模擬探討 DNA 核適體與小分子作用熱力學與結合機制
(The study of the binding thermodynamic and mechanism between DNA aptamer and small molecule by IsothermalTitration Calorimetry, Circular Dichroism and MolecularSimulation)
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摘要(中) 核適體(aptamer)是稀有且有功能性的核酸分子,對於其目標分子(ligand)具有親和性以及專一性。在過去幾年裡,許多高解析結構的aptamer複合物被解析出來,結合的模式與辨識的機制也慢慢被解開。然而,有些核適體複合物的結合行為與機制還不清楚尤其是缺乏結構資訊的分子。在本研究中,我們利用恆溫滴定卡計(ITC)以及圓二色光譜儀(CD)等的分析工具,並且配合上分子模擬的技術來研究DNA 核適體和小分子之間的反應作用機制。
本研究選擇了三個研究系統,第一個選擇的系統是已經有結構資訊的雙股DNA與一小分子藥物(daunomycin)的結合系統,利用此系統來確認我們整合ITC與CD的實驗分析的正確性。實驗結果顯示當溫度上升對反應的自由能更有利;且為反應熵所貢獻。而且,在daunomycin上的amine貢獻了靜電作用力而此促使了反應的進行。另外,在daunomycin-DNA的反應機制中也發現有焓熵補償效應。此研究方法,不僅僅符合了文獻的對此反應機制的推論,還能更深入的討論其反應機制。證明了ITC之熱力研究之合理性與其可能之貢獻。
進一步我們選擇了一個尚未被深入研究討論過而且未知結構的小分子胺基酸(L-Tyrosinamide;L-TyrNH2)以及其核適體之交互作用機制。由熱力學的資訊配合CD圖譜推論此反應行為為一個焓驅動的過程,並且核適體的結構由B-form 轉變為A-form。而這結果也說明了在L-Arm的反應過程也包含有induced-fit的反應機制。L-TyrNH2的amide group和phenolic hydroxyl group在此反應機制中扮演關鍵的角色。另外,值得注意的是Mg2+不僅增強反應的親和力而且幫助改變DNA 核適體的構型。
本研究最後對於核適體的一項值得受到重視的對掌性異構物的辨識做更深入的機制探討。選擇的是對L-argininamide已有少數幾篇研究以及初步的結構資訊,但對於D-form的研究卻完全沒有的DNA 核適體之結合機制的研究。利用我們的研究平台來深入研究DNA 核適體對於對掌性異構物( D和L-argininamide)的辨識機制。由熱力學研究發現L-Arm 和 D-Arm 和核適體的結合都是焓驅動且損失熵的過程,並且在L-Arm的反應過程也包含有induced-fit的反應機制。L-Arm 和 D-Arm 的 amino group的質子化參與靜電作用力且D-Arm與核適體的反應比L-Arm強。由兩異構物熱容量變化的相反趨勢,推測L-Arm 和 D-Arm與核適體結合可能在不同的結合位置而且造成不同構型的結合複合物。為了能夠由分子層面更深入了解核適體和其結合之ligand間的induced-fit的反應機制。我們利用explicit solvent分子動力學模擬(MD)來驗證在aptamer-L-Arm結合時參與的關鍵鹼基和在原子解析下的induced-fit binding過程。結果顯示在反應過程中,由C9與G10先與 L-Arm上的Guanidine作用,隨後A12與反方向的胺基作用,最後C17在和Guanidine作用完成結合程序。結構上aptamer-L-Arm經由一個induced-fit過程而達到一個幾何最佳化。此機制大致可以分成三個特徵階段︰吸附階段、結合反應階段、複合物穩定階段。另外,經由模擬的結果發現D-Arm、L-Arm與核適體的結合位置確實在不同位置,且由氫鍵與靜電作用能量分佈的分析發現D-Arm、L-Arm的反應機制也不太一樣。此結果也符合了實驗上的發現與推論。
本研究利用簡單、方便的研究方式有系統的探討一個DNA-小分子辨識系統。並且提供了aptamer-ligand結合機制的資訊,並且說明了在aptamer-ligand 結合路徑上的細部資訊。此研究的結果可以對於治療藥物的分子設計和分子辨識等分子工程上之應用提供更多的微觀機制資訊,且可結合NMR和X射線結晶學在結構分析的研究上,提供設計核適體辨識系統上的指導方針。
摘要(英) Aptamers are rare functional nucleic acids with binding affinity and specificity to target ligands. In past years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complexes interactions. However, aptamer complex binding behavior and mechanism are not clearly understood especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC), circular dichroism (CD) and molecular dynamics (MD) simulations were useful tools for studying the fundamental binding mechanism between DNA aptamers and small molecules. To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value were carried out.
In this study, we choose three DNA molecules to examine the binding behaviors between these DNA molecules and small ligands. The first system is to illustrate the binding mechanism of daunomycin binding with a simple dsDNA. The results suggest that the binding free energy more favorable with temperature increased; this is contributed by the binding entropy. Furthermore, the amine group on daunomycin contributes electrostatic interaction that induces the binding process. In addition, enthalpy–entropy compensation is also exhibited in the daunomycin–DNA binding mechanism.
Secondly, we examined the binding mechanism between L-Tyrosinamide (L-TyrNH2) and its aptamer. The thermodynamic signature along with the coupled CD spectral change suggests that this binding behavior is an enthalpy driven process. The results showed that the interaction is an induced fit binding. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg2+ not only improves binding affinity but also helps change the structure of DNA aptamer.
The last one is a comparative study of the DNA aptamer binding with L-argininamide (L-Arm) and its enantiomer (D-Arm). The thermodynamics study reveals that both L-Arm and D-Arm binding with the aptamer are an enthalpy driven and entropy cost process, and L-Arm binding with the aptamer involved induced-fit binding mechanism. The protonated amino group of both L-Arm and D-Arm participates in electrostatic interaction and this interaction is stronger for D-Arm than L-Arm binding with the aptamer. From the opposite behavior of the heat capacity change of the two enantiomers, we could suggest that L-Arm and D-Arm bind in different binding site of aptamer and resulted in different conformations of the binding complexes.
From previous studies, we found that induced-fit binding mechanism usually involved in the binding processes between aptamer and ligand. We used explicit solvent MD simulations to examine the critical bases involved in aptamer-L-Arm binding and the induced-fit binding process in atomic resolution. The simulation results revealed that three pairs of bases (C9-C16, G10-C16, and A12-C17) play important roles in aptamer-L-Arm binding and that aptamer-L-Arm binding adopts a geometry optimized through a general induced-fit process. The mechanism has the following characteristic stages: adsorption stage, binding stage and complex stabilization stage.
In addition, simulation results showed that the L-Arm binding location of the aptamer is different with D-Arm. From electrostatic interaction energy profile and hydrogen bonding analysis, the binding mechanisms of D-Arm and L-Arm are also different. These results are in agreement with the experiment inferences. This study used an easy, convenient method of performing a systemic study in recognition systems. This study also provides the information of aptamer-ligand binding mechanism, and shows the detail information of the binding pathway. It provides additional information about microscopic mechanisms useful for molecular design, molecular recognition, and the structural investigation from NMR and X-ray crystallography. This information can offer a guideline for molecular engineering in aptamer recognition design.
關鍵字(中) ★ 分子模擬
★ 核適體
★ 結合機制
★ 熱力學
關鍵字(英) ★ aptamer
★ binding mechanism
★ thermodynamic
★ molecular simulation
論文目次 摘要 i
Abstract iii
致謝 v
目錄 vii
圖目錄 xi
表目錄 xv
第一章 緒論 1
1.1研究動機 1
1.2研究目的 2
第二章 文獻回顧 5
2.1核酸簡介 5
2.2小分子與核酸作用 6
2.2.1溝槽結合 7
2.2.2崁入結合 8
2.3 RNA World Hypothesis 12
2.4核適體(Aptamer) 13
2.4.1 Systematic Evolution of Ligands by Exponential Enrichments(SELEX) 15
2.4.2核適體(Aptamer)與抗體(Antibody)之比較 17
2.4.3 Riboswitch 23
2.5核適體之相關應用 25
2.5.1 Biosensors與Signaling之應用 25
2.5.2 管柱層析與毛細管電泳之應用 27
2.5.3 藥物發展、治療與臨床之應用 28
2.5.4 奈米科技(nanotechnology)之應用 35
2.5.5 其他生醫上的研究應用 37
2.6 核適體應用上的瓶頸 39
2.7核適體與ligand結合行為 40
2.7.1 結構分析 40
2.7.2 統計實驗與演化分析 42
2.7.3 二級結構預測與序列最小化 43
2.7.4 動力學與熱力學分析 45
2.8分子動態模擬(MD) 48
2.8.1 基本計算原理 49
2.8.2 週期性邊界條件 50
2.8.3 分子力場 51
2.8.4 統計系集(ensemble) 59
第三章 實驗藥品與實驗方法 61
3.1 實驗藥品 61
3.2 儀器設備 62
3.3 實驗方法 62
3.3.1 恆溫滴定卡計 63
3.3.2 圓二色光譜儀 63
第四章 Daunomycin 與DNA的反應機制 65
4.1 摘要 65
4.2 前言 65
4.3 結果與討論 67
4.3.1溫度影響 67
4.3.2 鹽影響 69
4.3.3 pH值 72
4.3.4焓熵補償 74
4.4 結論 76
第五章 L-Tyrosinamide與核適體之反應機制 77
5.1 摘要 77
5.2 前言 77
5.3結果與討論 80
5.3.1 Circular Dichroism 80
5.3.2 溫度效應 82
5.3.3鹽濃度效應 86
5.3.4 pH值的影響與反應質子化過程 89
5.3.5 不同的類似物 92
5.3.6 Mg2+ 影響 93
5.4 結論 95
第六章 Argininamide與核適體之反應機制 97
6.1 摘要 97
6.2 前言 97
6.3結果 99
6.3.1 Circular Dichroism 99
6.3.2 Thermodynamic analysis 101
6.4 討論 109
6.5 結論 110
第七章 Argininamide與核適體反應機制之分子動態模擬 111
7.1 摘要 111
7.2 前言 111
7.3 實驗方法與分析 113
7.3.1 模擬系統 113
7.3.2 計算 114
7.3.3 座標分析 114
7.4 結果與討論 115
7.4.1 Arm-Aptamer Complex的平衡模擬 115
7.4.2 Arm-Free aptamer的平衡模擬 117
7.4.3 Induced-fit模擬結構分析 119
7.4.4 Induced-fit驅動力 125
7.4.5 D-, L-Argininamide form模擬比較分析 129
7.5 結論 135
第八章 總結 137
第九章 未來研究方向 139
第十章 References 141
第十一章 附錄 165
參考文獻 [1] Avery, O. T., Macleod, C. M., McCarty, M., Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types : Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type Iii. J Exp Med 1944, 79, 137-158.
[2] Hershey, A. D., Chase, M., Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 1952, 36, 39-56.
[3] Chargaff, E., Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 1950, 6, 201-209.
[4] Watson, J. D., Crick, F. H., Genetical implications of the structure of deoxyribonucleic acid. Nature 1953, 171, 964-967.
[5] Miller, S. L., A production of amino acids under possible primitive earth conditions. Science 1953, 117, 528-529.
[6] Oro, J., Mechanism of synthesis of adenine from hydrogen cyanide under possible primitive earth conditions. Nature 1961, 191, 1193-1194.
[7] Oro, J., Kamat, S. S., Amino-acid synthesis from hydrogen cyanide under possible primitive earth conditions. Nature 1961, 190, 442-443.
[8] Robertson, M. P., Miller, S. L., An efficient prebiotic synthesis of cytosine and uracil. Nature 1995, 375, 772-774.
[9] Miyakawa, S., Yamanashi, H., Kobayashi, K., Cleaves, H. J., Miller, S. L., Prebiotic synthesis from CO atmospheres: implications for the origins of life. Proc Natl Acad Sci U S A 2002, 99, 14628-14631.
[10] Orgel, L. E., Prebiotic adenine revisited: eutectics and photochemistry. Orig Life Evol Biosph 2004, 34, 361-369.
[11] Franklin, B. S., Ishizaka, S. T., Lamphier, M., Gusovsky, F., et al., Therapeutical targeting of nucleic acid-sensing Toll-like receptors prevents experimental cerebral malaria. Proc Natl Acad Sci U S A, 108, 3689-3694.
[12] Laurent, N., Sapet, C., Le Gourrierec, L., Bertosio, E., Zelphati, O., Nucleic acid delivery using magnetic nanoparticles: the Magnetofection??technology. Therapeutic Delivery, 2, 471-482.
[13] Hurley, L. H., DNA and its associated processes as targets for cancer therapy. Nat Rev Cancer 2002, 2, 188-200.
[14] Tse, W. C., Boger, D. L., Sequence-selective DNA recognition: natural products and nature's lessons. Chem Biol 2004, 11, 1607-1617.
[15] Wu, J., Liu, H., Duan, X., Ding, Y., et al., Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics 2009, 25, 30-35.
[16] Chaires, J. B., Energetics of drug-DNA interactions. Biopolymers 1997, 44, 201-215.
[17] Chaires, J. B., Drug--DNA interactions. Curr Opin Struct Biol 1998, 8, 314-320.
[18] Graves, D. E., Drug-DNA interactions. Methods Mol Biol 2001, 95, 161-169.
[19] Hurley, L. H., DNA and associated targets for drug design. J Med Chem 1989, 32, 2027-2033.
[20] Lerman, L. S., The structure of the DNA-acridine complex. Proc Natl Acad Sci U S A 1963, 49, 94-102.
[21] Siddiqui-Jain, A., Grand, C. L., Bearss, D. J., Hurley, L. H., Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci U S A 2002, 99, 11593-11598.
[22] Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., Dickerson, R. E., The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci U S A 1985, 82, 1376-1380.
[23] Mukherjee, A., Lavery, R., Bagchi, B., Hynes, J. T., On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes. J Am Chem Soc 2008, 130, 9747-9755.
[24] Wang, A. H., Ughetto, G., Quigley, G. J., Rich, A., Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution. Biochemistry 1987, 26, 1152-1163.
[25] Gottesfeld, J. M., Neely, L., Trauger, J. W., Baird, E. E., Dervan, P. B., Regulation of gene expression by small molecules. Nature 1997, 387, 202-205.
[26] White, S., Szewczyk, J. W., Turner, J. M., Baird, E. E., Dervan, P. B., Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 1998, 391, 468-471.
[27] Quintana, J. R., Lipanov, A. A., Dickerson, R. E., Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G. Biochemistry 1991, 30, 10294-10306.
[28] Rentzeperis, D., Marky, L. A., Dwyer, T. J., Geierstanger, B. H., et al., Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry 1995, 34, 2937-2945.
[29] Tewey, K. M., Rowe, T. C., Yang, L., Halligan, B. D., Liu, L. F., Adriamycin-induced DNA damage mediated by mammalian DNA topoisomerase II. Science 1984, 226, 466-468.
[30] Wilson, W. D., Ratmeyer, L., Zhao, M., Strekowski, L., Boykin, D., The search for structure-specific nucleic acid-interactive drugs: effects of compound structure on RNA versus DNA interaction strength. Biochemistry 1993, 32, 4098-4104.
[31] Hecht, S. M., The chemistry of activated bleomycin. Accounts of Chemical Research 1986, 19, 383-391.
[32] Kane, S. A., Hecht, S. M., Sun, J.-S., Garestier, T., Helene, C., Specific cleavage of a DNA triple helix by FeII.cntdot.bleomycin. Biochemistry 1995, 34, 16715-16724.
[33] Tan, J. D., Farinas, E. T., David, S. S., Mascharak, P. K., NMR Evidence of Sequence Specific DNA Binding by a Cobalt(III)-Bleomycin Analog with Tethered Acridine. Inorg Chem 1994, 33, 4295-4308.
[34] Sherman, S. E., Gibson, D., Wang, A. H., Lippard, S. J., X-ray structure of the major adduct of the anticancer drug cisplatin with DNA: cis-[Pt(NH3)2(d(pGpG))]. Science 1985, 230, 412-417.
[35] Arya, D. P., Coffee, R. L., Jr., DNA triple helix stabilization by aminoglycoside antibiotics. Bioorg Med Chem Lett 2000, 10, 1897-1899.
[36] Helene, C., The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des 1991, 6, 569-584.
[37] Lerman, L. S., Structural considerations in the interaction of DNA and acridines. J Mol Biol 1961, 3, 18-30.
[38] LePecq, J. B., Paoletti, C., A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization. J Mol Biol 1967, 27, 87-106.
[39] Krugh, T. R., Drug-DNA interactions. Curr Opin Struct Biol 1994, 4, 351-364.
[40] Nordmeier, E., Absorption spectroscopy and dynamic and static light-scattering studies of ethidium bromide binding to calf thymus DNA: implications for outside-binding and intercalation. J Phys Chem 1992, 96, 6045-6055.
[41] Qu, X., Wan, C., Becker, H. C., Zhong, D., Zewail, A. H., The anticancer drug-DNA complex: femtosecond primary dynamics for anthracycline antibiotics function. Proc Natl Acad Sci U S A 2001, 98, 14212-14217.
[42] Ren, J., Chaires, J. B., Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 1999, 38, 16067-16075.
[43] Van Dyke, M. W., Hertzberg, R. P., Dervan, P. B., Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). Proc Natl Acad Sci U S A 1982, 79, 5470-5474.
[44] Chan, L. M., McCarter, J. A., The interaction of aminoacridines with DNA. Biochim Biophys Acta 1970, 204, 252-254.
[45] Deubel, V., Leng, M., Interaction between proflavine and double stranded polynucleotides. Biochimie 1974, 56, 641-648.
[46] Löber, G., On the complex formation of acridine dyes with dna-iv. The equilibrium constants of substituted proflavine and acridine orange derivatives*. Photochemistry and Photobiology 1968, 8, 23-30.
[47] Drummond, D. S., Simpson-Gildemeister, V. F. W., Peacocke, A. R., Interaction of aminoacridines with deoxyribonucleic acid: Effects of ionic strength, denaturation, and structure. Biopolymers 1965, 3, 135-153.
[48] Riemer, S. C., Bloomfield, V. A., Effect of Mg++ and polyamines on proflavine binding to T2 DNA. Biopolymers 1979, 18, 1695-1708.
[49] Ortona, O., Costantino, L., Volpe, C. D., Vitagliano, V., Stacking equilibria of proflavine in various solutions. Journal of Molecular Liquids 1990, 45, 201-211.
[50] Quadrifoglio, F., Crescenzi, V., Giancotti, V., Calorimetry of DNA-dye interactions in aqueous solution : I. Proflavine and ethidium bromide. Biophys Chem 1974, 1, 319-324.
[51] Bloomfield, V. A., Crothers, D. M., Tinoco, I., Nucleic acids: structures, properties, and functions, University Science Books, Sausalito 2000.
[52] Jain, S. S., Anet, F. A., Stahle, C. J., Hud, N. V., Enzymatic behavior by intercalating molecules in a template-directed ligation reaction. Angew Chem Int Ed Engl 2004, 43, 2004-2008.
[53] Remeta, D. P., Mudd, C. P., Berger, R. L., Breslauer, K. J., Thermodynamic characterization of daunomycin-DNA interactions: comparison of complete binding profiles for a series of DNA host duplexes. Biochemistry 1993, 32, 5064-5073.
[54] Quigley, G. J., Wang, A. H., Ughetto, G., van der Marel, G., et al., Molecular structure of an anticancer drug-DNA complex: daunomycin plus d(CpGpTpApCpG). Proc Natl Acad Sci U S A 1980, 77, 7204-7208.
[55] Neidle, S., Taylor, G. L., Nucleic acid binding drugs. Some conformational properties of the anti-cancer drug daunomycin and several of its derivatives: implications for DNA-binding. FEBS Lett 1979, 107, 348-354.
[56] Gray, P. J., Phillips, D. R., Wedd, A. G., Photosensitized degradation of DNA by daunomycin. Photochem Photobiol 1982, 36, 49-57.
[57] Grimmond, H. E., Beerman, T., Alteration of chromatin structure induced by the binding of adriamycin, daunorubicin and ethidium bromide. Biochem Pharmacol 1982, 31, 3379-3386.
[58] Lown, J. W., Sim, S. K., Majumdar, K. C., Chang, R. Y., Strand scission of DNA by bound adriamycin and daunorubicin in the presence of reducing agents. Biochem Biophys Res Commun 1977, 76, 705-710.
[59] Someya, A., Tanaka, N., DNA strand scission induced by adriamycin and aclacinomycin A. J Antibiot (Tokyo) 1979, 32, 839-845.
[60] Center, M. S., Induction of single-strand regions in nuclear DNA by adriamycin. Biochem Biophys Res Commun 1979, 89, 1231-1238.
[61] Bodley, A., Liu, L. F., Israel, M., Seshadri, R., et al., DNA topoisomerase II-mediated interaction of doxorubicin and daunorubicin congeners with DNA. Cancer Res 1989, 49, 5969-5978.
[62] Nafziger, J., Auclair, C., Florent, J. C., Guillosson, J. J., Monneret, C., Pharmacological and physicochemical properties of a new anthracycline with potent antileukemic activity. Leuk Res 1991, 15, 709-713.
[63] Chaires, J. B., Dattagupta, N., Crothers, D. M., Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on interaction of daunomycin with deoxyribonucleic acid. Biochemistry 1982, 21, 3933-3940.
[64] Chaires, J. B., Fox, K. R., Herrera, J. E., Britt, M., Waring, M. J., Site and sequence specificity of the daunomycin-DNA interaction. Biochemistry 1987, 26, 8227-8236.
[65] Walter, A., Continuous mixing experiments allow to determine the size of binding sites for anthracyclines complexed to DNA. Biomed Biochim Acta 1985, 44, 1321-1327.
[66] Barthelemy-Clavey, V., Maurizot, J. C., Sicard, P. J., [Spectrophotometric study of the DNA-daunorubicin complex]. Biochimie 1973, 55, 859-868.
[67] Molinier-Jumel, C., Malfoy, B., Reynaud, J. A., Aubel-Sadron, G., Electrochemical study of DNA-anthracyclines interaction. Biochem Biophys Res Commun 1978, 84, 441-449.
[68] Zunino, F., Di Marco, A., Zaccara, A., Gambetta, R. A., The interaction of daunorubicin and doxorubicin with DNA and chromatin. Biochim Biophys Acta 1980, 607, 206-214.
[69] Zunino, F., Gambetta, R., Di Marco, A., Zaccara, A., Interaction of daunomycin and its derivatives with DNA. Biochim Biophys Acta 1972, 277, 489-498.
[70] Chaires, J. B., Thermodynamics of the daunomycin-DNA interaction: ionic strength dependence of the enthalpy and entropy. Biopolymers 1985, 24, 403-419.
[71] Chaires, J. B., Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides. Biochemistry 1983, 22, 4204-4211.
[72] Graves, D. E., Krugh, T. R., Adriamycin and daunorubicin bind in a cooperative manner to deoxyribonucleic acid. Biochemistry 1983, 22, 3941-3947.
[73] Lin, P. H., Kao, Y. H., Chang, Y., Cheng, Y. C., et al., Daunomycin interaction with DNA: microcalorimetric studies of the thermodynamics and binding mechanism. Biotechnol J 2010, 5, 1069-1077.
[74] Phillips, D. R., DiMarco, A., Zunino, F., The interaction of daunomycin with polydeoxynucleotides. Eur J Biochem 1978, 85, 487-492.
[75] Xodo, L. E., Manzini, G., Ruggiero, J., Quadrifoglio, F., On the interaction of daunomycin with synthetic alternating DNAs: sequence specificity and polyelectrolyte effects on the intercalation equilibrium. Biopolymers 1988, 27, 1839-1857.
[76] Chaires, J. B., Herrera, J. E., Waring, M. J., Preferential binding of daunomycin to 5'ATCG and 5'ATGC sequences revealed by footprinting titration experiments. Biochemistry 1990, 29, 6145-6153.
[77] Minotti, G., Sarvazyan, N., The anthracyclines: when good things go bad. Cardiovasc Toxicol 2007, 7, 53-55.
[78] Duncan, R., Kopeckova-Rejmanova, P., Strohalm, J., Hume, I., et al., Anticancer agents coupled to N-(2-hydroxypropyl)methacrylamide copolymers. I. Evaluation of daunomycin and puromycin conjugates in vitro. Br J Cancer 1987, 55, 165-174.
[79] Hudecz, F., Clegg, J. A., Kajtar, J., Embleton, M. J., et al., Synthesis, conformation, biodistribution, and in vitro cytotoxicity of daunomycin-branched polypeptide conjugates. Bioconjug Chem 1992, 3, 49-57.
[80] Miklan, Z., Orban, E., Csik, G., Schlosser, G., et al., New daunomycin-oligoarginine conjugates: synthesis, characterization, and effect on human leukemia and human hepatoma cells. Biopolymers 2009, 92, 489-501.
[81] Szabo, R., Banoczi, Z., Mezo, G., Lang, O., et al., Daunomycin-polypeptide conjugates with antitumor activity. Biochim Biophys Acta 2010, 1798, 2209-2216.
[82] Sprigg, L., Li, A., Choy, F. Y., Ausio, J., Interaction of daunomycin with acetylated chromatin. J Med Chem 2010, 53, 6457-6465.
[83] Yang, C., Choy, E., Hornicek, F. J., Wood, K. B., et al., Histone deacetylase inhibitor (HDACI) PCI-24781 potentiates cytotoxic effects of doxorubicin in bone sarcoma cells. Cancer Chemother Pharmacol.
[84] Gilbert, W., The {RNA} world. Nature 1986, 319.
[85] Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., et al., Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 1982, 31, 147-157.
[86] Joyce, G. F., Nonenzymatic template-directed synthesis of informational macromolecules. Cold Spring Harb Symp Quant Biol 1987, 52, 41-51.
[87] Joyce, G. F., RNA evolution and the origins of life. Nature 1989, 338, 217-224.
[88] Doudna, J. A., Couture, S., Szostak, J. W., A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science 1991, 251, 1605-1608.
[89] Doudna, J. A., Szostak, J. W., RNA-catalysed synthesis of complementary-strand RNA. Nature 1989, 339, 519-522.
[90] Uhlenbeck, O. C., A small catalytic oligoribonucleotide. Nature 1987, 328, 596-600.
[91] David, P. B., 5 Re-creating an RNA Replicase. CSH Monograph Archive: The RNA World, 2nd Ed. 1999, 37, 143-162.
[92] Barrick, J. E., Corbino, K. A., Winkler, W. C., Nahvi, A., et al., New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A 2004, 101, 6421-6426.
[93] Mandal, M., Breaker, R. R., Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 2004, 11, 29-35.
[94] Mandal, M., Lee, M., Barrick, J. E., Weinberg, Z., et al., A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004, 306, 275-279.
[95] Nahvi, A., Sudarsan, N., Ebert, M. S., Zou, X., et al., Genetic control by a metabolite binding mRNA. Chem Biol 2002, 9, 1043.
[96] Winkler, W., Nahvi, A., Breaker, R. R., Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419, 952-956.
[97] Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., Breaker, R. R., Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004, 428, 281-286.
[98] Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E., Breaker, R. R., An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol 2003, 10, 701-707.
[99] Breaker, R. R., Emilsson, G. M., Lazarev, D., Nakamura, S., et al., A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. RNA 2003, 9, 949-957.
[100] Carmi, N., Shultz, L. A., Breaker, R. R., In vitro selection of self-cleaving DNAs. Chem Biol 1996, 3, 1039-1046.
[101] Li, Y., Breaker, R. R., Phosphorylating DNA with DNA. Proc Natl Acad Sci U S A 1999, 96, 2746-2751.
[102] Li, Y., Breaker, R. R., Deoxyribozymes: new players in the ancient game of biocatalysis. Curr Opin Struct Biol 1999, 9, 315-323.
[103] Li, Y., Breaker, R. R., In vitro selection of kinase and ligase deoxyribozymes. Methods 2001, 23, 179-190.
[104] Flynn-Charlebois, A., Wang, Y., Prior, T. K., Rashid, I., et al., Deoxyribozymes with 2'-5' RNA ligase activity. J Am Chem Soc 2003, 125, 2444-2454.
[105] Purtha, W. E., Coppins, R. L., Smalley, M. K., Silverman, S. K., General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages. J Am Chem Soc 2005, 127, 13124-13125.
[106] Ellington, A. D., Szostak, J. W., In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818-822.
[107] Robertson, D. L., Joyce, G. F., Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 1990, 344, 467-468.
[108] Tuerk, C., Gold, L., Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505-510.
[109] Bunka, D. H., Stockley, P. G., Aptamers come of age - at last. Nat Rev Microbiol 2006, 4, 588-596.
[110] Breaker, R. R., Natural and engineered nucleic acids as tools to explore biology. Nature 2004, 432, 838-845.
[111] Cox, J. C., Hayhurst, A., Hesselberth, J., Bayer, T. S., et al., Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 2002, 30, e108.
[112] Cox, J. C., Rudolph, P., Ellington, A. D., Automated RNA selection. Biotechnol Prog 1998, 14, 845-850.
[113] Osborne, S. E., Ellington, A. D., Nucleic Acid Selection and the Challenge of Combinatorial Chemistry. Chem Rev 1997, 97, 349-370.
[114] Gopinath, S. C., Misono, T. S., Kawasaki, K., Mizuno, T., et al., An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J Gen Virol 2006, 87, 479-487.
[115] Nishikawa, F., Funaji, K., Fukuda, K., Nishikawa, S., In vitro selection of RNA aptamers against the HCV NS3 helicase domain. Oligonucleotides 2004, 14, 114-129.
[116] Sekiya, S., Noda, K., Nishikawa, F., Yokoyama, T., et al., Characterization and application of a novel RNA aptamer against the mouse prion protein. J Biochem 2006, 139, 383-390.
[117] Ciesiolka, J., Gorski, J., Yarus, M., Selection of an RNA domain that binds Zn2+. RNA 1995, 1, 538-550.
[118] Nieuwlandt, D., Wecker, M., Gold, L., In vitro selection of RNA ligands to substance P. Biochemistry 1995, 34, 5651-5659.
[119] Khati, M., Schuman, M., Ibrahim, J., Sattentau, Q., et al., Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2'F-RNA aptamers. J Virol 2003, 77, 12692-12698.
[120] Misono, T. S., Kumar, P. K., Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 2005, 342, 312-317.
[121] Pileur, F., Andreola, M. L., Dausse, E., Michel, J., et al., Selective inhibitory DNA aptamers of the human RNase H1. Nucleic Acids Res 2003, 31, 5776-5788.
[122] Berezovski, M. V., Musheev, M. U., Drabovich, A. P., Jitkova, J. V., Krylov, S. N., Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides. Nat Protoc 2006, 1, 1359-1369.
[123] Drabovich, A., Berezovski, M., Krylov, S. N., Selection of smart aptamers by equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM). J Am Chem Soc 2005, 127, 11224-11225.
[124] Mendonsa, S. D., Bowser, M. T., In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. Anal Chem 2004, 76, 5387-5392.
[125] Mendonsa, S. D., Bowser, M. T., In vitro selection of aptamers with affinity for neuropeptide Y using capillary electrophoresis. J Am Chem Soc 2005, 127, 9382-9383.
[126] Blank, M., Weinschenk, T., Priemer, M., Schluesener, H., Systematic Evolution of a DNA Aptamer Binding to Rat Brain Tumor Microvessels. Journal of Biological Chemistry 2001, 276, 16464-16468.
[127] Yang, X., Li, X., Prow, T. W., Reece, L. M., et al., Immunofluorescence assay and flow-cytometry selection of bead-bound aptamers. Nucleic Acids Res 2003, 31, e54.
[128] Eulberg, D., Buchner, K., Maasch, C., Klussmann, S., Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res 2005, 33, e45.
[129] Gopinath, S. C., Methods developed for SELEX. Anal Bioanal Chem 2007, 387, 171-182.
[130] Lee, J. F., Hesselberth, J. R., Meyers, L. A., Ellington, A. D., Aptamer database. Nucleic Acids Res 2004, 32, D95-100.
[131] Brockstedt, U., Uzarowska, A., Montpetit, A., Pfau, W., Labuda, D., In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochem Biophys Res Commun 2004, 313, 1004-1008.
[132] Geiger, A., Burgstaller, P., von der Eltz, H., Roeder, A., Famulok, M., RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 1996, 24, 1029-1036.
[133] Huizenga, D. E., Szostak, J. W., A DNA aptamer that binds adenosine and ATP. Biochemistry 1995, 34, 656-665.
[134] Kawakami, J., Imanaka, H., Yokota, Y., Sugimoto, N., In vitro selection of aptamers that act with Zn2+. J Inorg Biochem 2000, 82, 197-206.
[135] Koizumi, M., Breaker, R. R., Molecular recognition of cAMP by an RNA aptamer. Biochemistry 2000, 39, 8983-8992.
[136] Vianini, E., Palumbo, M., Gatto, B., In vitro selection of DNA aptamers that bind L-tyrosinamide. Bioorg Med Chem 2001, 9, 2543-2548.
[137] Zimmermann, G. R., Shields, T. P., Jenison, R. D., Wick, C. L., Pardi, A., A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA. Biochemistry 1998, 37, 9186-9192.
[138] Plummer, K. A., Carothers, J. M., Yoshimura, M., Szostak, J. W., Verdine, G. L., In vitro selection of RNA aptamers against a composite small molecule-protein surface. Nucleic Acids Res 2005, 33, 5602-5610.
[139] Pendergrast, P. S., Marsh, H. N., Grate, D., Healy, J. M., Stanton, M., Nucleic acid aptamers for target validation and therapeutic applications. J Biomol Tech 2005, 16, 224-234.
[140] Michaud, M., Jourdan, E., Ravelet, C., Villet, A., et al., Immobilized DNA aptamers as target-specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomers. Anal Chem 2004, 76, 1015-1020.
[141] Daniels, D. A., Chen, H., Hicke, B. J., Swiderek, K. M., Gold, L., A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc Natl Acad Sci U S A 2003, 100, 15416-15421.
[142] Hicke, B. J., Marion, C., Chang, Y. F., Gould, T., et al., Tenascin-C aptamers are generated using tumor cells and purified protein. J Biol Chem 2001, 276, 48644-48654.
[143] Nimjee, S. M., Rusconi, C. P., Sullenger, B. A., Aptamers: an emerging class of therapeutics. Annu Rev Med 2005, 56, 555-583.
[144] Breaker, R. R., Tech.Sight. Molecular biology. Making catalytic DNAs. Science 2000, 290, 2095-2096.
[145] Eaton, B. E., Pieken, W. A., Ribonucleosides and RNA. Annu Rev Biochem 1995, 64, 837-863.
[146] Floege, J., Ostendorf, T., Janssen, U., Burg, M., et al., Novel approach to specific growth factor inhibition in vivo: antagonism of platelet-derived growth factor in glomerulonephritis by aptamers. Am J Pathol 1999, 154, 169-179.
[147] Kopylov, A. M., Spiridonova, V. A., ChemInform Abstract: Combinatorial Chemistry of Nucleic Acids: SELEX. ChemInform 2001, 32, no-no.
[148] Kusser, W., Chemically modified nucleic acid aptamers for in vitro selections: evolving evolution. J Biotechnol 2000, 74, 27-38.
[149] Lee, J. F., Stovall, G. M., Ellington, A. D., Aptamer therapeutics advance. Curr Opin Chem Biol 2006, 10, 282-289.
[150] Nelson, J. S., Giver, L., Ellington, A. D., Letsinger, R. L., Incorporation of a non-nucleotide bridge into hairpin oligonucleotides capable of high-affinity binding to the Rev protein of HIV-1. Biochemistry 1996, 35, 5339-5344.
[151] Stoltenburg, R., Reinemann, C., Strehlitz, B., SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007, 24, 381-403.
[152] Cochrane, J. C., Strobel, S. A., Riboswitch effectors as protein enzyme cofactors. RNA 2008, 14, 993-1002.
[153] Corbino, K. A., Barrick, J. E., Lim, J., Welz, R., et al., Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol 2005, 6, R70.
[154] Batey, R. T., Structures of regulatory elements in mRNAs. Curr Opin Struct Biol 2006, 16, 299-306.
[155] Nudler, E., Mironov, A. S., The riboswitch control of bacterial metabolism. Trends Biochem Sci 2004, 29, 11-17.
[156] Tucker, B. J., Breaker, R. R., Riboswitches as versatile gene control elements. Curr Opin Struct Biol 2005, 15, 342-348.
[157] Vitreschak, A. G., Rodionov, D. A., Mironov, A. A., Gelfand, M. S., Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet 2004, 20, 44-50.
[158] Sudarsan, N., Barrick, J. E., Breaker, R. R., Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 2003, 9, 644-647.
[159] Gilbert, S. D., Stoddard, C. D., Wise, S. J., Batey, R. T., Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol 2006, 359, 754-768.
[160] Mironov, A. S., Gusarov, I., Rafikov, R., Lopez, L. E., et al., Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 2002, 111, 747-756.
[161] Winkler, W. C., Cohen-Chalamish, S., Breaker, R. R., An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A 2002, 99, 15908-15913.
[162] Grundy, F. J., Henkin, T. M., The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 1998, 30, 737-749.
[163] Miranda-Rios, J., Navarro, M., Soberon, M., A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc Natl Acad Sci U S A 2001, 98, 9736-9741.
[164] Gelfand, M. S., Mironov, A. A., Jomantas, J., Kozlov, Y. I., Perumov, D. A., A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet 1999, 15, 439-442.
[165] Franklund, C. V., Kadner, R. J., Multiple transcribed elements control expression of the Escherichia coli btuB gene. J Bacteriol 1997, 179, 4039-4042.
[166] Weinberg, Z., Barrick, J. E., Yao, Z., Roth, A., et al., Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res 2007, 35, 4809-4819.
[167] Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., et al., Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol 2010, 11, R31.
[168] Kim, J. N., Breaker, R. R., Purine sensing by riboswitches. Biol Cell 2008, 100, 1-11.
[169] Lee, J. O., So, H. M., Jeon, E. K., Chang, H., et al., Aptamers as molecular recognition elements for electrical nanobiosensors. Anal Bioanal Chem 2008, 390, 1023-1032.
[170] Liss, M., Petersen, B., Wolf, H., Prohaska, E., An aptamer-based quartz crystal protein biosensor. Anal Chem 2002, 74, 4488-4495.
[171] Baker, B. R., Lai, R. Y., Wood, M. S., Doctor, E. H., et al., An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. J Am Chem Soc 2006, 128, 3138-3139.
[172] Bang, G. S., Cho, S., Kim, B. G., A novel electrochemical detection method for aptamer biosensors. Biosens Bioelectron 2005, 21, 863-870.
[173] Ikebukuro, K., Kiyohara, C., Sode, K., Novel electrochemical sensor system for protein using the aptamers in sandwich manner. Biosens Bioelectron 2005, 20, 2168-2172.
[174] Lai, R. Y., Plaxco, K. W., Heeger, A. J., Aptamer-based electrochemical detection of picomolar platelet-derived growth factor directly in blood serum. Anal Chem 2007, 79, 229-233.
[175] Xiao, Y., Piorek, B. D., Plaxco, K. W., Heeger, A. J., A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. J Am Chem Soc 2005, 127, 17990-17991.
[176] Savran, C. A., Knudsen, S. M., Ellington, A. D., Manalis, S. R., Micromechanical detection of proteins using aptamer-based receptor molecules. Anal Chem 2004, 76, 3194-3198.
[177] Maehashi, K., Katsura, T., Kerman, K., Takamura, Y., et al., Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors. Anal Chem 2007, 79, 782-787.
[178] Nutiu, R., Li, Y., Structure-switching signaling aptamers. J Am Chem Soc 2003, 125, 4771-4778.
[179] Nutiu, R., Li, Y., Aptamers with fluorescence-signaling properties. Methods 2005, 37, 16-25.
[180] Yang, C. J., Jockusch, S., Vicens, M., Turro, N. J., Tan, W., Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc Natl Acad Sci U S A 2005, 102, 17278-17283.
[181] Navani, N. K., Li, Y., Nucleic acid aptamers and enzymes as sensors. Curr Opin Chem Biol 2006, 10, 272-281.
[182] Ravelet, C., Grosset, C., Peyrin, E., Liquid chromatography, electrochromatography and capillary electrophoresis applications of DNA and RNA aptamers. J Chromatogr A 2006, 1117, 1-10.
[183] Connor, A. C., McGown, L. B., Aptamer stationary phase for protein capture in affinity capillary chromatography. J Chromatogr A 2006, 1111, 115-119.
[184] Vo, T. U., McGown, L. B., Effects of G-quartet DNA stationary phase destabilization on fibrinogen peptide resolution in capillary electrochromatography. Electrophoresis 2006, 27, 749-756.
[185] Michaud, M., Jourdan, E., Villet, A., Ravel, A., et al., A DNA aptamer as a new target-specific chiral selector for HPLC. J Am Chem Soc 2003, 125, 8672-8679.
[186] Ruta, J., Ravelet, C., Grosset, C., Fize, J., et al., Enantiomeric separation using an l-RNA aptamer as chiral additive in partial-filling capillary electrophoresis. Anal Chem 2006, 78, 3032-3039.
[187] Pich, E. M., Epping-Jordan, M. P., Transgenic mice in drug dependence research. Ann Med 1998, 30, 390-396.
[188] Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., et al., Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411, 494-498.
[189] Hannon, G. J., RNA interference. Nature 2002, 418, 244-251.
[190] Blank, M., Blind, M., Aptamers as tools for target validation. Curr Opin Chem Biol 2005, 9, 336-342.
[191] Jellinek, D., Green, L. S., Bell, C., Lynott, C. K., et al., Potent 2'-amino-2'-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor. Biochemistry 1995, 34, 11363-11372.
[192] Purschke, W. G., Eulberg, D., Buchner, K., Vonhoff, S., Klussmann, S., An L-RNA-based aquaretic agent that inhibits vasopressin in vivo. Proc Natl Acad Sci U S A 2006, 103, 5173-5178.
[193] Klussmann, S., Nolte, A., Bald, R., Erdmann, V. A., Furste, J. P., Mirror-image RNA that binds D-adenosine. Nat Biotechnol 1996, 14, 1112-1115.
[194] Willis, M. C., Collins, B. D., Zhang, T., Green, L. S., et al., Liposome-anchored vascular endothelial growth factor aptamers. Bioconjug Chem 1998, 9, 573-582.
[195] Chang, S.-S., Shih, C.-W., Chen, C.-D., Lai, W.-C., Wang, C. R. C., The Shape Transition of Gold Nanorods. Langmuir 1998, 15, 701-709.
[196] Huang, C. C., Huang, Y. F., Cao, Z., Tan, W., Chang, H. T., Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. Anal Chem 2005, 77, 5735-5741.
[197] Pavlov, V., Xiao, Y., Shlyahovsky, B., Willner, I., Aptamer-functionalized Au nanoparticles for the amplified optical detection of thrombin. J Am Chem Soc 2004, 126, 11768-11769.
[198] Polsky, R., Gill, R., Kaganovsky, L., Willner, I., Nucleic acid-functionalized Pt nanoparticles: Catalytic labels for the amplified electrochemical detection of biomolecules. Anal Chem 2006, 78, 2268-2271.
[199] Levy, M., Cater, S. F., Ellington, A. D., Quantum-dot aptamer beacons for the detection of proteins. Chembiochem 2005, 6, 2163-2166.
[200] So, H. M., Park, D. W., Jeon, E. K., Kim, Y. H., et al., Detection and titer estimation of Escherichia coli using aptamer-functionalized single-walled carbon-nanotube field-effect transistors. Small 2008, 4, 197-201.
[201] Liu, J., Lu, Y., Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angewandte Chemie International Edition 2006, 45, 90-94.
[202] Liu, J., Mazumdar, D., Lu, Y., A simple and sensitive "dipstick" test in serum based on lateral flow separation of aptamer-linked nanostructures. Angew Chem Int Ed Engl 2006, 45, 7955-7959.
[203] Tu, S., Teng, Y. C., Yuan, C., Wu, Y. T., et al., The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. Nat Struct Mol Biol 2008, 15, 419-421.
[204] Kawakami, S., Hashida, M., Targeted delivery systems of small interfering RNA by systemic administration. Drug Metab Pharmacokinet 2007, 22, 142-151.
[205] Meade, B. R., Dowdy, S. F., Exogenous siRNA delivery using peptide transduction domains/cell penetrating peptides. Adv Drug Deliv Rev 2007, 59, 134-140.
[206] Convery, M. A., Rowsell, S., Stonehouse, N. J., Ellington, A. D., et al., Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. Nat Struct Biol 1998, 5, 133-139.
[207] Rowsell, S., Stonehouse, N. J., Convery, M. A., Adams, C. J., et al., Crystal structures of a series of RNA aptamers complexed to the same protein target. Nat Struct Biol 1998, 5, 970-975.
[208] Hermann, T., Patel, D. J., Adaptive recognition by nucleic acid aptamers. Science 2000, 287, 820-825.
[209] Desjardins, G., Bonneau, E., Girard, N., Boisbouvier, J., Legault, P., NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Research 2011.
[210] Noeske, J., Buck, J., Furtig, B., Nasiri, H. R., et al., Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res 2007, 35, 572-583.
[211] Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., et al., Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex. Nucleic Acids Res 2010, 38, 7822-7829.
[212] Carothers, J. M., Oestreich, S. C., Szostak, J. W., Aptamers selected for higher-affinity binding are not more specific for the target ligand. J Am Chem Soc 2006, 128, 7929-7937.
[213] Bishop, G. R., Ren, J., Polander, B. C., Jeanfreau, B. D., et al., Energetic basis of molecular recognition in a DNA aptamer. Biophys Chem 2007, 126, 165-175.
[214] Famulok, M., Molecular Recognition of Amino Acids by RNA-Aptamers: An L-Citrulline Binding RNA Motif and Its Evolution into an L-Arginine Binder. J Am Chem Soc 1994, 116, 1698-1706.
[215] Huang, Z., Szostak, J. W., Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer. RNA 2003, 9, 1456-1463.
[216] Cowperthwaite, M. C., Ellington, A. D., Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J Mol Evol 2008, 67, 95-102.
[217] Mannironi, C., Scerch, C., Fruscoloni, P., Tocchini-Valentini, G. P., Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA 2000, 6, 520-527.
[218] Sayer, N. M., Cubin, M., Rhie, A., Bullock, M., et al., Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem 2004, 279, 13102-13109.
[219] Dey, A. K., Griffiths, C., Lea, S. M., James, W., Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA 2005, 11, 873-884.
[220] Huang, Z., Wang, X., Gao, G., Analyses of SELEX-derived ZAP-binding RNA aptamers suggest that the binding specificity is determined by both structure and sequence of the RNA. Protein Cell 2010, 1, 752-759.
[221] Anderson, P. C., Mecozzi, S., Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity. Nucleic Acids Res 2005, 33, 6992-6999.
[222] Muller, M., Weigand, J. E., Weichenrieder, O., Suess, B., Thermodynamic characterization of an engineered tetracycline-binding riboswitch. Nucleic Acids Res 2006, 34, 2607-2617.
[223] Ha, J. H., Capp, M. W., Hohenwalter, M. D., Baskerville, M., Record, M. T., Jr., Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions. J Mol Biol 1992, 228, 252-264.
[224] Andre, C., Xicluna, A., Guillaume, Y. C., Aptamer-oligonucleotide binding studied by capillary electrophoresis: cation effect and separation efficiency. Electrophoresis 2005, 26, 3247-3255.
[225] Kulshina, N., Edwards, T. E., Ferre-D'Amare, A. R., Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA 2010, 16, 186-196.
[226] Record, M. T., Jr., Anderson, C. F., Lohman, T. M., Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys 1978, 11, 103-178.
[227] Suryawanshi, H., Sabharwal, H., Maiti, S., Thermodynamics of peptide-RNA recognition: the binding of a Tat peptide to TAR RNA. J Phys Chem B 2010, 114, 11155-11163.
[228] Neves, M. A., Reinstein, O., Saad, M., Johnson, P. E., Defining the secondary structural requirements of a cocaine-binding aptamer by a thermodynamic and mutation study. Biophys Chem, 153, 9-16.
[229] Buck, M., Bouguet-Bonnet, S., Pastor, R. W., MacKerell, A. D., Jr., Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J 2006, 90, L36-38.
[230] Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., et al., A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J Am Chem Soc 1995, 117, 5179-5197.
[231] Lin, F., Wang, R., Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems. Journal of Chemical Theory and Computation 2010, 6, 1852-1870.
[232] Crow, R. T., Crothers, D. M., Inhibition of topoisomerase I by anthracycline antibiotics: evidence for general inhibition of topoisomerase I by DNA-binding agents. J Med Chem 1994, 37, 3191-3194.
[233] Denny, W. A., Baguley, B. C., Dual topoisomerase I/II inhibitors in cancer therapy. Curr Top Med Chem 2003, 3, 339-353.
[234] Ferguson, L. R., Denny, W. A., Genotoxicity of non-covalent interactions: DNA intercalators. Mutat Res 2007, 623, 14-23.
[235] Snyder, R. D., Hendry, L. B., Toward a greater appreciation of noncovalent chemical/DNA interactions: application of biological and computational approaches. Environ Mol Mutagen 2005, 45, 100-105.
[236] Zou, Y., Ling, Y. H., Reddy, S., Priebe, W., Perez-Soler, R., Effect of vesicle size and lipid composition on the in vivo tumor selectivity and toxicity of the non-cross-resistant anthracycline annamycin incorporated in liposomes. Int J Cancer 1995, 61, 666-671.
[237] Dignam, J. D., Qu, X., Ren, J., Chaires, J. B., Daunomycin binding to detergent micelles: a model system for evaluating the hydrophobic contribution to drug-DNA interactions. J Phys Chem B 2007, 111, 11576-11584.
[238] Frederick, C. A., Williams, L. D., Ughetto, G., van der Marel, G. A., et al., Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin. Biochemistry 1990, 29, 2538-2549.
[239] Bouma, J., Beijnen, J. H., Bult, A., Underberg, W. J., Anthracycline antitumour agents. A review of physicochemical, analytical and stability properties. Pharm Weekbl Sci 1986, 8, 109-133.
[240] Remeta, D. P., Mudd, C. P., Berger, R. L., Breslauer, K. J., Thermodynamic characterization of daunomycin-DNA interactions: microcalorimetric measurements of daunomycin-DNA binding enthalpies. Biochemistry 1991, 30, 9799-9809.
[241] Record, M. T., Jr., Ha, J. H., Fisher, M. A., Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol 1991, 208, 291-343.
[242] Chaires, J. B., Satyanarayana, S., Suh, D., Fokt, I., et al., Parsing the free energy of anthracycline antibiotic binding to DNA. Biochemistry 1996, 35, 2047-2053.
[243] Ren, J., Jenkins, T. C., Chaires, J. B., Energetics of DNA intercalation reactions. Biochemistry 2000, 39, 8439-8447.
[244] Lin, F. Y., Chen, W. Y., Hearn, M. T., 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, 3875-3883.
[245] Lin, P. H., Yen, S. L., Lin, M. S., Chang, Y., et al., Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer. J Phys Chem B 2008, 112, 6665-6673.
[246] Seelig, J., Ganz, P., Nonclassical hydrophobic effect in membrane binding equilibria. Biochemistry 1991, 30, 9354-9359.
[247] Haq, I., Thermodynamics of drug-DNA interactions. Arch Biochem Biophys 2002, 403, 1-15.
[248] Luedtke, N. W., Carmichael, P., Tor, Y., Cellular uptake of aminoglycosides, guanidinoglycosides, and poly-arginine. J Am Chem Soc 2003, 125, 12374-12375.
[249] Nguyen, B., Stanek, J., Wilson, W. D., Binding-linked protonation of a DNA minor-groove agent. Biophys J 2006, 90, 1319-1328.
[250] Barbieri, C. M., Pilch, D. S., Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study. Biophys J 2006, 90, 1338-1349.
[251] Leavitt, S., Freire, E., Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr Opin Struct Biol 2001, 11, 560-566.
[252] Fukada, H., Takahashi, K., Sturtevant, J. M., Differential scanning calorimetric study of the thermal unfolding of Taka-amylase A from Aspergillus oryzae. Biochemistry 1987, 26, 4063-4068.
[253] Fukada, H., Takahashi, K., Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins 1998, 33, 159-166.
[254] Gilli, P., Ferretti, V., Gilli, G., Enthalpy-Entropy Compensation in Drug-Receptor Binding. J. Phys. Chem. 1994, 98, 1515-1518.
[255] Jensen, W. A., Armstrong, J. M., De Giorgio, J., Hearn, M. T., Thermodynamic analysis of the stabilisation of pig heart mitochondrial malate dehydrogenase and maize leaf phosphoenolpyruvate carboxylase by different salts, amino acids and polyols. Biochim Biophys Acta 1997, 1338, 186-198.
[256] Liu, L., Yang, C., Guo, Q. X., A study on the enthalpy-entropy compensation in protein unfolding. Biophys Chem 2000, 84, 239-251.
[257] Cornish-Bowden, A., Enthalpy-entropy compensation: a phantom phenomenon. J Biosci 2002, 27, 121-126.
[258] Starikov, E. B., Norden, B., Enthalpy-entropy compensation: a phantom or something useful? J Phys Chem B 2007, 111, 14431-14435.
[259] Krug, R. R., Hunter, W. G., Grieger, R. A., Statistical interpretation of enthalpy-entropy compensation. Nature 1976, 361, 566-567.
[260] Krug, R. R., Hunter, W. G., Grieger, R. A., Enthalpy-entropy compensation. 1. Some fundamental statistical problems associated with the analysis of van't Hoff and Arrhenius data. J. Phys. Chem. 1976, 80, 2335-2341.
[261] Krug, R. R., Hunter, W. G., Grieger, R. A., Enthalpy-entropy compensation. 2. Separation of the chemical from the statistical effect. J. Phys. Chem. 1976, 80, 2341-2351.
[262] Yu, H., Ren, J., Chaires, J. B., Qu, X., Hydration of drug-DNA complexes: greater water uptake for adriamycin compared to daunomycin. J Med Chem 2008, 51, 5909-5911.
[263] Leung, D. H., Bergman, R. G., Raymond, K. N., Enthalpy-entropy compensation reveals solvent reorganization as a driving force for supramolecular encapsulation in water. J Am Chem Soc 2008, 130, 2798-2805.
[264] Brodsky, A. S., Williamson, J. R., Solution structure of the HIV-2 TAR-argininamide complex. J Mol Biol 1997, 267, 624-639.
[265] Montange, R. K., Batey, R. T., Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006, 441, 1172-1175.
[266] Sui, G., Soohoo, C., Affar el, B., Gay, F., et al., A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci U S A 2002, 99, 5515-5520.
[267] Bozza, M., Sheardy, R. D., Dilone, E., Scypinski, S., Galazka, M., Characterization of the secondary structure and stability of an RNA aptamer that binds vascular endothelial growth factor. Biochemistry 2006, 45, 7639-7643.
[268] Pilch, D. S., Kaul, M., Barbieri, C. M., Kerrigan, J. E., Thermodynamics of aminoglycoside-rRNA recognition. Biopolymers 2003, 70, 58-79.
[269] Kaul, M., Barbieri, C. M., Kerrigan, J. E., Pilch, D. S., Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: elucidation of the number of drug amino groups involved and their identities. J Mol Biol 2003, 326, 1373-1387.
[270] Kankia, B. I., Marky, L. A., Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration. J Am Chem Soc 2001, 123, 10799-10804.
[271] Eble, J. E., Grob, R. L., Antle, P. E., Snyder, L. R., Simplified description of high-performance liquid chromatographic separation under overload conditions, based on the Craig distribution model: II. Effect of isotherm type, and experimental verification of computer simulations for a single band. J Chromatogr A 1987, 384, 45-79.
[272] Shuman, C. F., Hamalainen, M. D., Danielson, U. H., Kinetic and thermodynamic characterization of HIV-1 protease inhibitors. J Mol Recognit 2004, 17, 106-119.
[273] W. Curtis Johnson, J., Determination of the conformation of nucleic acid by electronic CD, in: Fasman, G. D. (Ed.), Circular Dichroism and the Conformational Analysis of Biomolecules, Plenum Press, New York 1996, p. 433.
[274] Merino, E. J., Weeks, K. M., Facile conversion of aptamers into sensors using a 2'-ribose-linked fluorophore. J Am Chem Soc 2005, 127, 12766-12767.
[275] Leulliot, N., Varani, G., Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 2001, 40, 7947-7956.
[276] Williamson, J. R., Induced fit in RNA-protein recognition. Nat Struct Biol 2000, 7, 834-837.
[277] Liggins, J. R., Privalov, P. L., Energetics of the specific binding interaction of the first three zinc fingers of the transcription factor TFIIIA with its cognate DNA sequence. Proteins 2000, Suppl 4, 50-62.
[278] Privalov, P. L., Jelesarov, I., Read, C. M., Dragan, A. I., Crane-Robinson, C., The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5. J Mol Biol 1999, 294, 997-1013.
[279] Spolar, R. S., Record, M. T., Jr., Coupling of local folding to site-specific binding of proteins to DNA. Science 1994, 263, 777-784.
[280] Tamura, A., Privalov, P. L., The entropy cost of protein association. J Mol Biol 1997, 273, 1048-1060.
[281] Ha, J. H., Spolar, R. S., Record, M. T., Jr., Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J Mol Biol 1989, 209, 801-816.
[282] Thomas, J. R., Liu, X., Hergenrother, P. J., Biochemical and thermodynamic characterization of compounds that bind to RNA hairpin loops: toward an understanding of selectivity. Biochemistry 2006, 45, 10928-10938.
[283] Cowan, J. A., Ohyama, T., Wang, D., Natarajan, K., Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions. Nucleic Acids Res 2000, 28, 2935-2942.
[284] Gold, B., Effect of cationic charge localization on DNA structure. Biopolymers 2002, 65, 173-179.
[285] Manning, G. S., Comments on selected aspects of nucleic acid electrostatics. Biopolymers 2003, 69, 137-143.
[286] McDonald, R. J., Dragan, A. I., Kirk, W. R., Neff, K. L., et al., DNA bending by charged peptides: electrophoretic and spectroscopic analyses. Biochemistry 2007, 46, 2306-2316.
[287] Baumann, C. G., Smith, S. B., Bloomfield, V. A., Bustamante, C., Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci U S A 1997, 94, 6185-6190.
[288] Levitt, M., How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc Natl Acad Sci U S A 1978, 75, 640-644.
[289] Hagerman, P. J., Flexibility of DNA. Annu Rev Biophys Biophys Chem 1988, 17, 265-286.
[290] Parker, M. H., Lunney, E. A., Ortwine, D. F., Pavlovsky, A. G., et al., Analysis of the binding of hydroxamic acid and carboxylic acid inhibitors to the stromelysin-1 (matrix metalloproteinase-3) catalytic domain by isothermal titration calorimetry. Biochemistry 1999, 38, 13592-13601.
[291] Petrosian, S. A., Makhatadze, G. I., Contribution of proton linkage to the thermodynamic stability of the major cold-shock protein of Escherichia coli CspA. Protein Sci 2000, 9, 387-394.
[292] Fersht, A. R., Blow, D. M., Fastrez, J., Leaving group specificity in the chymotrypsin-catalyzed hydrolysis of peptides. A stereochemical interpretation. Biochemistry 1973, 12, 2035-2041.
[293] Sundaresan, N., Suresh, C. H., A Base-Sugar??hosphate Three-Layer ONIOM Model for Cation Binding:??Relative Binding Affinities of Alkali Metal Ions for Phosphate Anion in DNA. Journal of Chemical Theory and Computation 2007, 3, 1172-1182.
[294] Deng, Q., Watson, C. J., Kennedy, R. T., Aptamer affinity chromatography for rapid assay of adenosine in microdialysis samples collected in vivo. J Chromatogr A 2003, 1005, 123-130.
[295] Yamauchi, T., Miyoshi, D., Kubodera, T., Nishimura, A., et al., Roles of Mg2+ in TPP-dependent riboswitch. FEBS Lett 2005, 579, 2583-2588.
[296] Hud, N. V., Plavec, J., A unified model for the origin of DNA sequence-directed curvature. Biopolymers 2003, 69, 144-158.
[297] Hud, N. V., Polak, M., DNA-cation interactions: The major and minor grooves are flexible ionophores. Curr Opin Struct Biol 2001, 11, 293-301.
[298] Andre, C., Berthelot, A., Thomassin, M., Guillaume, Y. C., Enantioselective aptameric molecular recognition material: Design of a novel chiral stationary phase for enantioseparation of a series of chiral herbicides by capillary electrochromatography. Electrophoresis 2006, 27, 3254-3262.
[299] Soto, A. M., Kankia, B. I., Dande, P., Gold, B., Marky, L. A., Incorporation of a cationic aminopropyl chain in DNA hairpins: thermodynamics and hydration. Nucleic Acids Res 2001, 29, 3638-3645.
[300] Gubitz, G., Schmid, M. G., Chiral separation by chromatographic and electromigration techniques. A review. Biopharm Drug Dispos 2001, 22, 291-336.
[301] Higuchi, A., Higuchi, Y., Furuta, K., Yoon, B. O., et al., Chiral separation of phenylalanine by ultrafiltration through immobilized DNA membranes. Journal of Membrane Science 2003, 221, 207-218.
[302] Higuchi, A., Yomogita, H., Yoon, B. O., Kojima, T., et al., Optical resolution of amino acid by ultrafiltration using recognition sites of DNA. Journal of Membrane Science 2002, 205, 203-212.
[303] Hamada, H., Shiraki, K., L-argininamide improves the refolding more effectively than L-arginine. J Biotechnol 2007, 130, 153-160.
[304] Brumbt, A., Ravelet, C., Grosset, C., Ravel, A., et al., Chiral stationary phase based on a biostable L-RNA aptamer. Anal Chem 2005, 77, 1993-1998.
[305] Harada, K., Frankel, A. D., Identification of two novel arginine binding DNAs. EMBO J 1995, 14, 5798-5811.
[306] Piatigorskaia, T. L., Evdokimov Iu, M., Varshavskii Ia, M., [Compact form of synthetic polynucleotides. Relationship between secondary structure and circular dichroism spectra]. Mol Biol (Mosk) 1978, 12, 404-412.
[307] Lin, C. H., Patel, D. J., Encapsulating an amino acid in a DNA fold. Nat Struct Biol 1996, 3, 1046-1050.
[308] Gallagher, K., Sharp, K., Electrostatic contributions to heat capacity changes of DNA-ligand binding. Biophys J 1998, 75, 769-776.
[309] Calnan, B., Tidor, B., Biancalana, S., Hudson, D., Frankel, A., Arginine-mediated RNA recognition: the arginine fork. Science 1991, 252, 1167-1171.
[310] Weigand, J. E., Suess, B., Aptamers and riboswitches: perspectives in biotechnology. Appl Microbiol Biotechnol 2009, 85, 229-236.
[311] Fischer, E., Einfluss der Configuration auf die Wirkung der Enzyme. Berichte der deutschen chemischen Gesellschaft 1894, 27, 2985-2993.
[312] Koshland, D. E., Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A 1958, 44, 98-104.
[313] Bosshard, H. R., Molecular recognition by induced fit: how fit is the concept? News Physiol Sci 2001, 16, 171-173.
[314] Csermely, P., Palotai, R., Nussinov, R., Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 2010, 35, 539-546.
[315] Lin, P. H., Tong, S. J., Louis, S. R., Chang, Y., Chen, W. Y., Thermodynamic basis of chiral recognition in a DNA aptamer. Phys Chem Chem Phys 2009, 11, 9744-9750.
[316] Rowe, A. A., Miller, E. A., Plaxco, K. W., Reagentless measurement of aminoglycoside antibiotics in blood serum via an electrochemical, ribonucleic acid aptamer-based biosensor. Anal Chem 2010, 82, 7090-7095.
[317] Lim, J., Winkler, W. C., Nakamura, S., Scott, V., Breaker, R. R., Molecular-recognition characteristics of SAM-binding riboswitches. Angew Chem Int Ed Engl 2006, 45, 964-968.
[318] Blouin, S., Mulhbacher, J., Penedo, J. C., Lafontaine, D. A., Riboswitches: ancient and promising genetic regulators. Chembiochem 2009, 10, 400-416.
[319] Huang, W., Kim, J., Jha, S., Aboul-ela, F., A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Research 2009.
[320] Schmeing, T. M., Huang, K. S., Strobel, S. A., Steitz, T. A., An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 2005, 438, 520-524.
[321] Tao, J., Frankel, A. D., Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 1996, 35, 2229-2238.
[322] Robertson, S. A., Harada, K., Frankel, A. D., Wemmer, D. E., Structure determination and binding kinetics of a DNA aptamer-argininamide complex. Biochemistry 2000, 39, 946-954.
[323] Pitici, F., Beveridge, D. L., Baranger, A. M., Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity? Biopolymers 2002, 65, 424-435.
[324] Verli, H., Guimaraes, J. A., Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations. J Mol Graph Model 2005, 24, 203-212.
[325] Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., et al., The Amber biomolecular simulation programs. J Comput Chem 2005, 26, 1668-1688.
[326] Phillips, J. C., Braun, R., Wang, W., Gumbart, J., et al., Scalable molecular dynamics with NAMD. J Comput Chem 2005, 26, 1781-1802.
[327] Essmann, U., Perera, L., Berkowitz, M., Darden, T., et al., A smooth particle mesh Ewald method. J Chem Phys 1995, 103, 8577-8593.
[328] Ryckaert, J.-P., Ciccotti, G., Berendsen, H. J. C., Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys 1977, 23, 327-341.
[329] Villa, A., Wohnert, J., Stock, G., Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res 2009, 37, 4774-4786.
指導教授 陳文逸(Wen-Yih Chen) 審核日期 2011-6-28
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