Aptamers in the virologists' toolkit

Journal of General Virology

Volumn 88, Issue 2, 2007, Pages 351-364

  James, Williams ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; APTAMER; BEVACIZUMAB; CAPSID PROTEIN; DNA POLYMERASE; ENFUVIRTIDE; LENTIVIRUS VECTOR; MICROBICIDE; MONOCLONAL ANTIBODY; NUCLEIC ACID; PEGAPTANIB; RANIBIZUMAB; RETROVIRUS VECTOR; RIBONUCLEASE; RIBOZYME; RNA DIRECTED DNA POLYMERASE; SHORT HAIRPIN RNA; SINGLE STRANDED DNA; TRANSACTIVATOR PROTEIN; VIRUS ENVELOPE PROTEIN; VIRUS ENZYME; VIRUS RNA;

AEROSOL; APPLIED RESEARCH; BINDING AFFINITY; BIOSENSOR; CLINICAL TRIAL; COLORECTAL CANCER; CONDOM; CREAM; DNA REPLICATION; DRUG EFFICACY; DRUG SAFETY; ENZYME ACTIVITY; GENE DELIVERY SYSTEM; GENE EXPRESSION REGULATION; GENE TECHNOLOGY; HEPATITIS C VIRUS; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN T CELL LEUKEMIA VIRUS 1; INFLUENZA; LOW DRUG DOSE; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RETINA MACULA DEGENERATION; RETINA MACULA EDEMA; REVIEW; RNA BINDING; RNA STRUCTURE; SEQUENCE ANALYSIS; UNSPECIFIED SIDE EFFECT; VAGINA PESSARY; VIRAL GENE THERAPY; VIRION; VIRUS GENOME; VIRUS INHIBITION; VIRUS REPLICATION; VIRUS VIRULENCE;

ANTIVIRAL AGENTS; APTAMERS, NUCLEOTIDE; HUMANS; SELEX APTAMER TECHNIQUE; VIROLOGY; VIRUS DISEASES; VIRUS REPLICATION; VIRUSES;

EID: 33846840878     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.82442-0     Document Type: Review

References (120)

1. Adamis, A. P., Altaweel, M., Bressler, N. M., Cunningham, E. T., Jr, Davis, M. D., Goldbaum, M., Gonzales, C., Guyer, D. R., Barrett, K. & Patel, M. (2006). Changes in retinal neovascularization after pegaptanib (Macugen) therapy in diabetic individuals. Macugen Diabetic Retinopathy Study Group. Ophthalmology 113, 23-28.
2. Aldaz-Carroll, L., Tallet, B., Dausse, E., Yurchenko, L. & Toulme, J. J. (2002). Apical loop-internal loop interactions: a new RNA-RNA recognition motif identified through in vitro selection against RNA hairpins of the hepatitis C virus mRNA. Biochemistry 41, 5883-5893.
3. Andreola, M. L., Pileur, F., Calmels, C., Ventura, M., Tarrago-Litvak, L., Toulme, J. J. & Litvak, S. (2001). DNA aptamers selected against the HfV-1 RNase H display in vitro antiviral activity. Biochemistry 40, 10087-10094.
4. Aurup, H., Williams, D. M. & Eckstein, F. (1992). 2′-Fluoro- and 2′- amino-2′-deoxynudeoside 5′-triphosphates as substrates for T7 RNA polymerase. Biochemistry 31, 9636-9641.
5. Avery, R. L., Pieramici, D. J., Rabena, M. D., Castellarin, A. A., Nasir, M. A. & Giust M. J. (2006). Intravitreal bevacizumab (Avastin) for neovascular age-related macular degeneration. Ophthalmology 113, 363-372.
6. Bachler, M., Schroeder, R. & von Ahsen, U. (1999). StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA 5, 1509-1516.
7. Bai, J., Banda, N., Lee, N. S., Rossi, J. & Akkina, R. (2002). RNA- based anti-HIV-1 gene therapeutic constructs in SCID-hu mouse model. Mol Ther 6, 770-782.
8. Banerjea, A., Li, M. J., Remling, L., Rossi, J. & Akkina, R. (2004). Lentiviral transduction of Tar Decoy and CCR5 ribozyme into CD34+ progenitor cells and derivation of HIV-1 resistant T cells and macrophages. AIDS Res Ther 1, 2.
9. Bartel, D. P., Zapp, M. L., Green, M. R. & Szostak, J. W. (1991). HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67, 529-536.
10. Baskerville, S., Zapp, M. & Ellington, A. D. (1995). High-resolution mapping of the human T-cell leukemia virus type 1 Rex-binding element by in vitro selection. J Virol 69, 7559-7569.
11. Baskerville, S., Zapp, M. & Ellington, A. D. (1999). Anti-Rexaptamers as mimics of the Rex-binding element. J Virol 73, 4962-4971.
12. Beaurain, F., Di Primo, C., Toulme, J. J. & Laguerre, M. (2003). Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer. Nucleic Acids Res 31, 4275-4284.
13. Bellecave, P., Andreola, M. L., Ventura, M., Tarrago-Litvak, L., Litvalf, S. & Astier-Gin, T. (2003). Selection of DNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus and inhibit viral RNA synthesis in vitro. Oligonucleotides 13, 455-463.
14. Berglund, J. A., Charpentier, B. & Rosbash, M. (1997). A high affinity binding site for the HIV-1 nucleocapsid protein. Nucleic Acids Res 25, 1042-1049.
15. Biroccio, A., Hamm, J., Incitti, L, De Francesco, R. & Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity ligands of the hepatitis C virus RNA-dependent RNA polymerase. J Virol 76, 3688-3696.
16. Boiziau, C., Dausse, E., Yurchenko, L. & Toulme, J. J. (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. J Biol Chem 274, 12730-12737.
17. Bunka, D. H. & Stockley, P. G. (2006). Aptamers come of age - at last. Nat Rev Microbiol 4, 588-596.
18. Burke, D. H., Scates, L., Andrews, K. & Gold, L. (1996). Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J Mol Biol 264, 650-666.
19. Chakravarthy, U., Adamis, A. P., Cunningham, E. T., Jr, Goldbaum, M., Guyer, D. R., Katz, B. & Patel, M. (2006a). Year 2 efficacy results of 2 randomized controlled clinical trials of pegaptanib for neovascular age-related macular degeneration. VEGF Inhibition Study in Ocular Neovascularization (V.I.S.I.O.N.) Clinical Trial Group. Ophthalmology 113, 1508.
20. Chakravarthy, U., Soubrane, G., Bandello, F., Chong, V., Creuzot- Garcher, C., Dimitrakos, S. A., II, Korobelnik, J. F., Larsen, M., Mones, J. & other authors (2006b). Evolving European guidance on the medical management of neovascular age related macular degeneration. Br J Ophthalmol 90, 1188-1196.
21. Chaloin, L., Lehmann, M. J., Sczakiel, G. & Restle, T. (2002). Endogenous expression of a high-affinity pseudoknot RNA aptamer suppresses replication of HIV-1. Nucleic Acids Res 30, 4001-4008.
22. Chen, H. & Gold, L. (1994). Selection of high-affinity RNA ligands to reverse transcriptase: inhibition of cDNA synthesis and RNase H activity. Biochemistry 33, 8746-8756.
23. Chen, H., McBroom, D. G., Zhu, Y. O., Gold, L. & North, T. W. (1996). Inhibitory RNA ligand to reverse transcriptase from feline immunodeficiency virus. Biochemistry 35, 6923-6930.
24. Chen, Y., Wiesmann, C., Fuh, G., Li, B., Christinger, H. W., McKay, P., de Vos, A. M. & Lowman, H. B. (1999). Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity- matured Fab in complex with antigen. J Mol Biol 293, 865-881.
25. Cho, S., Lee, S. H., Chung, W. J., Kim, Y. K., Lee, Y. S. & Kim, B. G. (2004). Microbead-based affinity chromatography chip using RNA aptamer modified with photocleavable linker. Electrophoresis 25, 3730-3739.
26. Cho, S., Kim, J. E., Lee, B. R., Kim, J. H. & Kim, B. G. (2005). Bisaptazyme sensors for hepatitis C virus replicase and helicase without blank signal. Nucleic Acids Res 33, e177.
27. Clever, J. L., Taplitz, R. A., Lochrie, M. A., Polisky, B. & Parslow, T. G. (2000). A heterologous, high-affinity RNA ligand for human immunodeficiency virus Gag protein has RNA packaging activity. J Virol 74, 541-546.
28. Collin, D., van Heijenoort, C., Boiziau, C., Touime, J. J. & Guittet, E. (2000). NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer. Nucleic Acids Res 28, 3386-3391.
29. Convery, M. A., Rowsell, S., Stonehouse, N. J., Ellington, A. D., Hirao, I., Murray, J. B., Peabody, D. S., Phillips, S. E. & Stockley, P. G. (1998). Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. Nat Struct Biol 5, 133-139.
30. Cunningham, E. T., Jr, Adamis, A. P., Altaweel, M., Aiello, L. P., Bressler, N. M., D'Amico, D. J., Goldbaum, M., Guyer, D. R., Katz, B. & other authors (2005). A phase II randomized double-masked trial of pegaptanib, an anti-vascular endothelial growth factor aptamer, for diabetic macular edema. Ophthalmology 112, 1747-1757.
31. D'Amico, D. J., Patel, M., Adamis, A. P., Cunningham, E. T., Jr, Guyer, D. R. & Katz, B. (2006). Pegaptanib sodium for neovascular age-related macular degeneration: two-year safety results of the two prospective, multicenter, controlled clinical trials. VEGF Inhibition Study in Ocular Neovascularization (V.I.S.I.O.N.) Clinical Trial Group. Ophthalmology 113, 1001.
32. Dangerfield, J. A., Windbichier, N., Salmons, B., Gunzburg, W. H. & Schroder, R. (2006). Enhancement of the StreptoTag method for isolation of endogenously expressed proteins with complex RNA binding targets. Electrophoresis 27, 1874-1877.
33. Darfeuille, F., Hansen, J. B., Orum, H., Di Primo, C. & Toulme, J. J. (2004). LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1. Nucleic Acids Res 32, 3101-3107.
34. Da Rocha Gomes, S., Dausse, E. & Toulme, J. J. (2004). Determinants of apical loop-internal loop RNA-RNA interactions involving the HCV IRES. Biochem Biophys Res Commun 322, 820-826.
35. DeStefano, J. J. & Cristofaro, J. V. (2006). Selection of primer- template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity. Nucleic Acids Res 34, 130-139.
36. Day, A. K., Griffiths, C., Lea, S. M. & James, W. (2005a). Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA 11, 873-884.
37. Dey, A. K., Khati, M., Tang, M., Wyatt, R., Lea, S. M. & James, W. (2005b). An aptamer that neutralizes R5 strains of human immunodeficiency virus type 1 blocks gp120-CCR5 interaction. J Virol 79, 13806-13810.
38. Duconge, F. & Toulme, J. J. (1999). In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA 5, 1605-1614.
39. Ellington, A. D. & Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
40. Fisher, T. S., Joshi, P. & Prasad, V. R. (2005). HIV-1 reverse transcriptase mutations that confer decreased in vitro susceptibility to anti-RT DNA aptamer RT1t49 confer cross resistance to other anti-RT aptamers but not to standard RT inhibitors. AIDS Res Ther 2, 8.
41. Fitzwater, T. & Polisky, B. (1996). A SELEX primer. Methods Enzymol 267, 275-301.
42. Fu, H., Guthrie, J. W. & Le, X. C. (2006). Study of binding stoichiometries of the human immunodeficiency virus type 1 reverse transcriptase by capillary electrophoresis and laser-induced fluorescence polarization using aptamers as probes. Electrophoresis 27, 433-441.
43. Fukuda, K., Vishinuvardhan, D., Sekiya, S., Kakiuchi, N., Shimotohno, K, Kumar, P. K. & Nishikawa, S. (1997). Specific RNA aptamers to NS3 protease domain of hepatitis C virus. Nucleic Acids Symp Ser 37, 237-238.
44. Fukuda, K., Vishnuvardhan, D., Sekiya, S., Hwang, J., Kakiuchi, N., Taira, K., Shimotohno, K., Kumar, P. K. & Nishikawa, S. (2000). Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. Eur J Biochem 267, 3685-3694.
45. Fukuda, K., Umehara, T., Sekiya, S., Kunio, K, Hasegawa, T. & Nishikawa, S. (2004). An RNA ligand inhibits hepatitis C virus NS3 protease and helicase activities. Biochern Biophys Res Commun 325, 670-675.
46. Giver, L., Bartel, D., Zapp, M., Pawul, A., Green, M. & Ellington, A. D. (11993). Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res 21, 5509-5516.
47. Good, P. D., Krikos, A. J., Li, S. X., Bertrand, E., Lee, N. S., Giver, L., Ellington, A., Zaia, J. A., Rossi, J. J. & Engelke, D. R. (1997). Expression of small, therapeutic RNAs in human cell nuclei. Gene Ther 4, 45-54.
48. Gopinath, S. C., Sakamaki, Y., Kawasaki, K. & Kumar, P. K. (2006a). An efficient RNA aptamer against human influenza B virus hemagglutinin. J Biochem (Tokyo) 139, 837-846.
49. Gopinath, S. C. B., Misono, T. S., Kawasaki, K, Mizuno, T., Imai, M., Odagiri, T. & Kumar, P. K. R. (2006b). An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J Gen Virol 87, 479-487.
50. Gragoudas, E. S., Adamis, A. P., Cunningham, E. T., Jr, Feinsod, M. & Guyer, D. R. (2004). Pegaptanib for neovascular age-related macular degeneration. VEGF Inhibition Study in Ocular Neovascularization Clinical Trial Group. N Engl J Med 351, 2805-2816.
51. Green, L. S., Jellinek, D., Bell, C., Beebe, L. A., Feistner, B. D., Gill, S. C., Jucker, F. M. & Janjic, N. (1995). Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor. Chem Biol 2, 683-695.
52. Guo, S., Tschammer, N., Mohammed, S. & Guo, P. (2005). Specific delivery of therapeutic RNAs to cancer cells via the dimerization mechanism of phi29 motor pRNA. Hum Gene Ther 16, 1097-1109.
53. Hannoush, R. N., Carriero, S., Min, K. L. & Damha, M. J. (2004). Selective inhibition of HIV-1 reverse transcriptase (HIV-1 RT) RNase H by small RNA hairpins and dumbbells. ChemBioChern 5, 527-533.
54. Hansen, J. A., Wang, J., Kawde, A. N., Xiang, Y., Gothelf, K. V. & Collins, G. (2006). Quantum-dot/aptamer-based ultrasensitive multi-analyte electrochemical biosensor. J Am Chem Soc 128, 2228-2229.
55. Heier, J. S., Antoszyk, A. N., Pavan, P. R., Leff, S. R., Rosenfeld, P. J., Ciulla, T. A., Dreyer, R. F., Gentile, R. C., Sy, J. P. & other authors (2006). Ranibizumab for treatment of neovascular age-related macular degeneration: a phase I/II multicenter, controlled, multidose study. Ophthalmology 113, 642.
56. Held, D. M., Kissel, J. D., Saran, D., Michalowski, D. & Burke, D. H. (2006). Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication. J Biol Chem 281, 25712-25722.
57. Horn, W. T., Convery, M. A., Stonehouse, N. J., Adams, C. J., Liljas, L., Phillips, S. E. & Stockley, P. G. (2004). The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA inter- actions. RNA 10, 1776-1782.
58. Hwang, J., Fauzi, H., Fukuda, K., Sekiya, S., Kakiuchi, N., Shimotohno, K., Taira, K., Kusakabe, I. & Nishikawa, S. (2000). The RNA aptamer-binding site of hepatitis C virus NS3 protease. Biochern Biophys Res Commun 279, 557-562.
59. James, W. (2000). Aptamers. In Encyclopedia of Analytical Chemistry. Applications, Theory and Instrumentation, pp. 4848-4871. Edited by R. A. Meyers. Chichester, UK: Wiley.
60. James, W. (2001). Nucleic acid and polypeptide aptamers: a powerful approach to ligand discovery. Curr Opin Pharmacol 1, 540-546.
61. Jellinek, D., Green, L. S., Bell, C. & Janjic, N. (1994). Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor. Biochemistry 33, 10450-10456.
62. Jensen, K. B., Green, L., MacDougal-Waugh, S. & Tuerk, C. (1994). Characterization of an in vitro-selected RNA ligand to the HIV-I Rev protein. J Mol Biol 235, 237-247.
63. Jeon, S. H., Kayhan, B., Ben-Yedidia, T. & Amon, R. (2004). A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J Biol Chem 279, 48410-48419.
64. Jiang, F., Gorin, A., Hu, W., Majumdar, A., Baskerville, S., Xu, W., Ellington, A. & Patel, D. J. (1999). Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples. Structure 7, 1461-1472.
65. Jing, N. & Hogan, M. E. (1998). Structure-activity of tetrad-forming oligonucleotides as a potent anti-HIV therapeutic drug. J Biol Chem 273, 34992-34999.
66. Jing, N., Rando, R. F., Pommier, Y. & Hogan, M. E. (1997). Ion selective folding of loop domains in a potent anti-HIV oligonucleotide. Biochemistry 36, 12498-12505.
67. Joshi, P. & Prasad, V. R. (2002). Potent inhibition of human immunodeficiency virus type 1 replication by template analog reverse transcriptase inhibitors derived by SELEX (systematic evolution of ligands by exponential enrichment). J Virol 76, 6545-6557.
68. Joshi, P. J., North, T. W. & Prasad, V. R. (2005). Aptarners directed to HIV-1 reverse transcriptase display greater efficacy over small hairpin RNAs targeted to viral RNA in blocking HIV-1 replication. Mol Ther 11, 677-686.
69. Khati, M., Schuman, M., Ibrahim, J., Saftentau, Q., Gordon, S. & James, W. (2003). Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2′F-RNA aptamers. J Virol 77, 12692-12698.
70. Kikuchi, K., Umehara, T., Fukuda, K., Hwang, J., Kuno, A., Hasegawa, T. & Nishikawa, S. (2003). RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region. J Biochem (Tokyo) 133, 263-270.
71. Kikuchi, K., Umehara, T., Fukuda, K., Kuno, A., Hasegawa, T. & Nishikawa, S. (2005). A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId. Nucleic Acids Res 33, 683-692.
72. Kim, M. Y. & Jeong, S. (2003). RNA aptamers that bind the nucleocapsid protein contain pseudoknots. Mol Cells 16, 413-417.
73. Kim, M. Y. & Jeong, S. (2004). Inhibition of the functions of the nucleocapsid protein of human immunodeficiency virus-1 by an RNA aptamer. Biochem Biophys Res Commun 320, 1181-1186.
74. Kim, S. J., Kim, M. Y., Lee, J. H., You, J. C. & Jeong, S. (2002). Selection and stabilization of the RNA aptamers against the human immunodeficiency virus type-1 nucleocapsid protein. Biochem Biophys Res Commun 291, 925-931.
75. Kolb, G., Reigadas, S., Boiziau, C., van Aerschot, A., Arzumanov, A., Gait, M. J., Herdewijn, P. & Toulme, J. J. (2005). Hexitol nucleic acid- containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 44, 2926-2933.
76. Kumar, P. K., Machida, K, Urvil, P. T., Kakiuchi, N., Vishnuvardhan, D., Shimotohno, K., Taira, K. & Nishikawa, S. (1997). Isolation of RNA aptamers specific to the NS3 protein of hepatitis C virus from a pool of completely random RNA. Virology 237, 270-282.
77. Lee, J.-H., Canny, M. D., De Erkenez, A., Krilleke, D., Ng, Y.-S., Shima, D. T., Pardi, A. & Jucker, F. (2005). A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165. Proc Natl Acad Sci U S A 102, 18902-18907.
78. Liss, M., Petersen, B., Wolf, H. & Prohaska, E. (2002). An aptamer- based quartz crystal protein biosensor. Anal Chem 74, 4488-4495.
79. Lochrie, M. A., Waugh, S., Pratt, D. G., Jr, Clever, J., Parslow, T. G. & Polisky, B. (1997). In vitro selection of RNAs that bind to the burnan immunodeficiency virus type-1 gag polyprotein. Nucleic Acids Res 25, 2902-2910.
80. Marozzi, A., Meneveri, R., Giacca, M., Gutierrez, M. I., Siccardi, A. G. & Ginelli, E. (1998). In vitro selection of HIV-1 TAR variants by the Tat protein. J Biotechnol 61, 117-128.
81. Matsugami, A., Kobayashi, S., Ouhashi, K., Uesugi, S., Yamamoto, R., Taira, K, Nishikawa, S., Kumar, P. K. & Katahira, M. (2003). Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer. Structure 11, 533-545.
82. Misono, T. S. & Kumar, P. K. (2005). Selection of RNA aptamers; against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 342, 312-317.
83. Muller, Y. A., Chen, Y., Christinger, H. W., Li, B., Cunningham, B. C., Lowman, H. B. & de Vos, A. M. (1998). VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Structure 6, 1153-1167.
84. Nickens, D. G., Patterson, J. T. & Burke, D. H. (2003). Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli. RNA 9, 1029-1033.
85. Nishikawa, F., Kakiuchi, N., Funaji, K., Fukuda, K., Sekiya, S. & Nishikawa, S. (2003). Inhibition of HCV NS3 protease by RNA aptamers in cells. Nucleic Acids Res 31, 1935-1943.
86. Nishikawa, F., Funaji, K., Fukuda, K. & Nishikawa, S. (2004). In vitro selection of RNA aptamers against the HCV NS3 helicase domain. Oligonucleotides 14, 114-129.
87. Parrott, A. M., Lago, H., Adams, C. J., Ashcroft, A. E., Stonehouse, N. J. & Stockley, P. G. (2000). RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour. Nucleic Acids Res 28, 489-497.
88. Pavski, V. & Le, X. C. (2001). Detection of human immunodeficiency virus type 1 reverse transcriptase using aptamers as probes in affinity capillary electrophoresis. Anal Chem 73, 6070-6076.
89. Pestourie, C., Tavitian, B. & Duconge, F. (2005). Aptamers; against extracellular targets for in vivo applications. Biochimie 87, 921-930.
90. Piguet, V. & Sattentau, O. (2004). Dangerous liaisons at the virological synapse. J Clin Invest 114, 605-610.
91. Puglisi, J. D., Chen, L., Blanchard, S. & Frankel, A. D. (1995). Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270, 1200-1203.
92. Rhodes, A. & James, W. (1990). Inhibition of human immunodeficiency virus replication in cell culture by endogenously synthesized antisense RNA. J Gen Virol 71, 1965-1974.
93. Rittner, K., Burmester, C. & Sczakiel, G. (1993). In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1. Nucleic Acids Res 21, 1381-1387.
94. Romero-Lopez, C., Barroso-delJesus, A., Puerta-Fernandez, E. & Berzal-Herranz, A. (2005). Interfering with hepatitis C virus IRES activity using RNA molecules identified by a novel in vitro selection method. Biol Chem 386, 183-190.
95. Rosenfeld, P. J., Rich, R. M. & Lalwani, G. A. (2006a). Ranibizumab: phase III clinical trial results. Ophthalmol Clin North Am 19, 361-372.
96. Rosenfeld, P. J., Heier, J. S., Hantsbarger, G. & Shams, N. (2006b). Tolerability and efficacy of multiple escalating doses of ranibizumab (Lucentis) for neovascular age-related macular degeneration. Ophthalmology 113, 632.e1.
97. Rowsell, S., Stonehouse, N. J., Convery, M. A., Adams, C. J., Ellington, A. D., Hirao, I., Peabody, D. S., Stockley, P. G. & Phillips, S. E. (1998). Crystal structures of a series of RNA aptamers complexed to the same protein target. Nat Struct Biol 5, 970-975.
98. Ruckman, J., Green, L. S., Beeson, J., Waugh, S., Gillette, W. L., Henninger, D. D., Claesson-Welsh, L. & Janjic, N. (1998). 2′- Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain. J Biol Chem 273, 20556-20567.
99. Sayer, N., Ibrahim, J., Turner, K., Tahiri-Alaoui, A. & James, W. (2002). Structural characterization of a 2′F-RNA aptamer that binds a HIV-1 SU glycoprotein, gp120. Biochem Biophys Res Commun 293, 924-931.
100. Schneider, D., Tuerk, C. & Gold, L. (1992). Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J Mol Biol 228, 862-869.
101. Schneider, D. J., Felgon, J., Hostomsky, Z. & Gold, L. (1995). High- affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 34, 9599-9610.
102. Sekiya, S., Nishikawa, F., Fukuda, K. & Nishikawa, S. (2003). Structure/ function analysis of an RNA aptamer for hepatitis C virus NS3 protease. J Biochem (Tokyo) 133, 351-359.
103. Southern, E. M., Case-Green, S. C., Elder, J. K., Johnson, M., Mir, K. U., Wang, L. & Williams, J. C. (1994). Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res 22, 1368-1373.
104. Srisawat, C. & Engelke, D. R. (2001). Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins. RNA 7, 632-641.
105. Sullenger, B. A., Gallardo, H. F., Lingers, G. E. & Gilboa, E. (1990). Overexpression of TAR sequences renders cells resistant to human immunodeficiency virus replication. Cell 63, 601-608.
106. Tahiri-Alaoui, A., Frigotto, L., Manville, N., Ibrahim, J., Romby, P. & James, W. (2002). High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands. Nucleic Acids Res 30, e45.
107. Tian, Y., Adya, N., Wagner, S., Giam, C. Z., Green, M. R. & Ellington, A. D. (1995). Dissecting protein:protein interactions between transcription factors with an RNA aptamer. RNA 1, 317-326.
108. Tombelli, S., Minunni, M., Luzi, E. & Mascini, M. (2005). Aptamer- based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 67, 135-141.
109. Tuerk, C. & Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
110. Tuerk, C. & MacDougal-Waugh, S. (1993). In vitro evolution of functional nucleic acids: higl-affinity RNA ligands of HIV-1 proteins. Gene 137, 33-39.
111. Tuerk, C., MacDougal, S. & Gold, L. (1992). RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci U S A 89, 6988-6992.
112. Umehara, T., Fukuda, K., Nishikawa, F., Kohara, M., Hasegawa, T. & Nishikawa, S. (2005). Rational design of dual-functional aptamers that inhibit the protease and helicase activities of HCV NS3. J Biochem (Tokyo) 137, 339-347.
113. Urvil, P. T., Kakiuchi, N., Zhou, D. M., Shimotohno, K., Kumar, P. K. & Nishikawa, S. (1997). Selection of RNA aptamers that bind specifically to the NS3 protease of hepatitis C virus. Eur J Biochem 248, 130-138.
114. van den Worm, S. H., Stonehouse, N. J., Valegard, K., Murray, J. B., Walton, C., Fridborg, K., Stockley, P. G. & Liljas, L. (1998). Crystal structures of MS2 coat protein mutants in complex with wild- type RNA operator fragments. Nucleic Acids Res 26, 1345-1351.
115. Vo, N.V., Oh, J.W. & Lai, M. M. (2003). Identification of RNAligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates. Virology 307, 301-316.
116. Wilkinson, T. A., Zhu, L., Hu, W. & Chen, Y. (2004). Retention of conformational flexibility in HIV-1 Rev-RNA complexes. Biochemistry 43, 16153-16160.
117. Wilson, C., Nix, J. & Szostak, J. (1998). Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry 37, 14410-14419.
118. Yamamoto, R., Katahira, M., Nishikawa, S., Baba, T., Taira, K & Kumar, P. K. (2000). A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the transactivation by Tat of transcription in vitro and in vivo. Genes Cells 5, 371-388.
119. Ye, X., Gorin, A., Ellington, A. D. & Patel, D. J. (1996). Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex. Nat Struct Biol 3, 1026-1033.
120. Ye, X., Gorin, A., Frederick, R., Hu, W., Majumdar, A., Xu, W., McLendon, G., Ellington, A. & Patel, D. J. (1999). RNA architecture dictates the conformations of a bound peptide. Chem Biol 6, 657-669.