Aptamers in virology: Recent advances and challenges

Frontiers in Microbiology

Volumn 3, Issue FEB, 2012, Pages

  Binning, Jennifer M ^a,b   Leung, Daisy W ^a   Amarasinghe, Gaya K ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

Aptamer; Research tools; Structural virology; Therapeutic and diagnostic agents

Indexed keywords

EID: 84868659577     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2012.00029     Document Type: Article

References (52)

1. Aldaz-Carroll, L., Tallet, B., Dausse, E., Yurchenko, L., and 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.
2. Bellecave, P., Andreola, M. L., Ventura, M., Tarrago-Litvak, L., Litvak, S., and Astier-Gin, T. (2003). Selection of DNA aptamers that bind the RNA-dependentRNApolymerase of hepatitis C virus and inhibit viral RNA synthesis in vitro. Oligonu-cleotides 13,455-463.
3. Bellecave, P., Cazenave, C., Rumi, J., Staedel, C., Cosnefroy, O., Andreola, M. L., Ventura, M., Tarrago-Litvak, L., and Astier-Gin, T. (2008). Inhibition of hepatitis C virus (HCV) RNA polymerase by DNA aptamers: mechanism of inhibition of in vitro RNA synthesis and effect on HCV-infected cells. Antimicrob. Agents Chemother. 52, 2097-2110.
4. Biroccio, A., Hamm, J., Incitti, I., De Francesco, R., and Tomei, L. (2002). Selection of RNA aptamers that are specific and high-affinity lig-ands of the hepatitis C virus RNA-dependent RNA polymerase.J. Virol. 76,3688-3696.
5. Bunka, D. H., and Stockley, P. G. (2006). Aptamers come of age-at last. Nat. Rev. Microbiol. 4, 588-596.
6. Chang, H. C., Samaniego, F., Nair, B. C., Buonaguro, L., andEnsoli, B. (1997). HIV-1 Tat protein exits from cells via a leaderless secretory pathway and binds to extracellular matrix-associated heparan sulfate proteo-glycans through its basic region. AIDS 11, 1421-1431.
7. Chelliserrykattil, J., and Ellington, A. D. (2004). Evolution of a T7 RNA polymerase variant that transcribes 2'-O-methyl RNA. Nat. Biotechnol. 22, 1155-1160.
8. Da Rocha Gomes, S., Dausse, E., and Toulme, J. J. (2004). Determinants of apical loop-internal loop RNA-RNA interactions involving the HCV IRES. Biochem. Biophys. Res. Com-mun. 322, 820-826.
9. Davis, K. A., Lin, Y., Abrams, B., and Jayasena, S. D. (1998). Staining of cell surface human CD4 with 2/-i7-pyrimidine-containing RNA aptamers for flow cytometry. Nucleic Acids Res. 26, 3915-3924.
10. Dey, A. K., Griffiths, C., Lea, S. M., and James, W. (2005a). Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA 11, 873-884.
11. Dey, A. K., Khati, M., Tang, M., Wyatt, R., Lea, S. M., and James, W. (2005b). An aptamer that neutralizes R5 strains of human immunodeficiency virus type 1 blocks gp120-CCR5 interaction.J. Virol. 79, 13806-13810.
12. Dhar,G.S.,andDatta,A. (2009).Targeting pseudoknots in H5N1 hemag-glutinin using designed aptamers. Bioinformation 4, 193-196.
13. Ellington, A. D., and Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
14. Fang, X., Cao, Z., Beck, T., and Tan, W. (2001). Molecular aptamer for realtime oncoprotein platelet-derived growth factor monitoring by fluorescence anisotropy. Anal. Chem. 73, 5752-5757.
15. Fletcher, S. J., Phillips, L. W., Milli-gan, A. S., and Rodda, S. J. (2010). Toward specific detection of Dengue virus serotypes using a novel modular biosensor. Biosens. Bioelectron. 26,1696-1700.
16. Gopinath, S. C. (2007). Antiviral aptamers. Arch. Virol. 152, 2137-2157.
17. Gopinath, S. C. (2008). Anti-coagulant aptamers. Thromb. Res. 122, 838-847.
18. Gopinath, S. C., Misono, T. S., Kawasaki, K., Mizuno, T., Imai, M., Odagiri, T., and Kumar, P. K. (2006). An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J. Gen. Virol. 87, 479-487.
19. James, W. (2001). Nucleic acid and polypeptide aptamers: a powerful approach to ligand discovery. Curr. Opin. Pharmacol. 1, 540-546.
20. James, W. (2007). Aptamers in the virologists' toolkit./Gen. Virol. 88, 351-364.
21. Jayasena, S. D. (1999). Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45, 1628-1650.
22. Jellinek, D., Green, L. S., Bell, C., Lynott, C. K., Gill, N., Vargeese, C., Kirschenheuter, G., Mcgee, D. P., Abesinghe, P., Pieken, W. A., Shapiro, R., Rifkin, D. B., Moscatelli, D., and Janjic, N. (1995). Potent 2'-amino-2'-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor. Biochemistry 34, 11363-11372.
23. Jeon, S. H., Kayhan, B., Ben-Yedidia, T., and Arnon, R. (2004). A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J. Biol. Chem. 279, 48410-48419.
24. Jhaveri, S., Rajendran, M., and Ellington, A. D. (2000). In vitro selection of signaling aptamers. Nat. Biotechnol. 18, 1293-1297.
25. Kanamori, H., Yuhashi, K., Uchiyama, Y., Kodama, T., and Ohnishi, S. (2009). In vitro selection of RNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus: a possible role of GC-rich RNA motifs in NS5B binding. Virology 388, 91-102.
26. Kato, Y., Minakawa, N., Komatsu, Y., Kamiya, H., Ogawa, N., Harashima, H., and Matsuda, A. (2005). New NTP analogs: the synthesis of 4'-thioUTP and 4'-thioCTP and their utility for SELEX. Nucleic Acids Res. 33,2942-2951.
27. Kikuchi, K., Umehara, T., Fukuda, K., Hwang, J., Kuno, A., Hasegawa, T., and Nishikawa, S. (2003). RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region./Biochem. 133, 263-270.
28. Kikuchi, K., Umehara, T., Fukuda, K., Kuno, A., Hasegawa, T., and 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.
29. Kikuchi, K., Umehara, T., Nishikawa, F., Fukuda, K., Hasegawa, T., and Nishikawa, S. (2009). Increased inhibitory ability of conjugated RNA aptamers against the HCV IRES. Biochem. Biophys. Res. Commun. 386, 118-123.
30. Kim,S.J.,Kim,M.Y.,Lee,J.H.,You,J.C., and 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.
31. Liu, J., Yang, Y., Hu, B., Ma, Z. Y., Huang, H. P., Yu, Y., Liu, S. P., Lu, M. J., and Yang, D. L. (2010). Development of HBsAg-binding aptamers that bind HepG2.2.15 cells via HBV surface antigen. Virol. Sin. 25, 27-35.
32. Meyer, C., Hahn, U., and Rentmeis-ter,A. (2011). Cell-specific aptamers as emerging therapeutics. J Nucleic Acids 2011, 904750.
33. Minunni, M., Tombelli, S., Gullotto, A., Luzi, E., and Mascini, M. (2004). Development of biosensors with aptamers as bio-recognition element: the case of HIV-1 Tat protein. Biosens. Bioelectron. 15, 1149-1156.
34. Misono, T. S., and Kumar, P. K. (2005). Selection of RNA aptamers against human influenza virus hemagglutinin using surface plas-mon resonance. Anal. Biochem. 342, 312-317.
35. Mucha, P., Szyk, A., Rekowski, P., and Barciszewski, J. (2002). Structural requirements for conserved Arg52 residue for interaction of the human immunodeficiency virus type 1 trans-activation responsive element with trans-activator of transcription protein (49-57). Capillary electrophoresis mobility shift assay. J. Chromatogr. A 968, 211-220.
36. Neff, C. P., Zhou, J., Remling, L., Kuruvilla, J., Zhang, J., Li, H., Smith, D. D., Swiderski, P., Rossi, J. J., and Akkina, R. (2011). An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4(+) T cell decline in humanized mice. Sci. Transl Med. 3, 66ra66.
37. O'Sullivan, C. K. (2002). Aptasensors-the future of biosensing? Anal. Bioanal. Chem. 372, 44-48.
38. Park, S. Y., Kim, S., Yoon, H., Kim, K. B., Kalme, S. S., Oh, S., Song, C. S., and Kim, D. E. (2011). Selection of an antiviral RNA aptamer against hemagglutinin of the subtype H5 avian influenza virus. Nucleic Acid Ther. 21, 395-402.
39. Ramalingam, D., Duclair, S., Datta, S. A., Ellington, A., Rein, A., and Prasad, V. R. (2011). RNA aptamers directed to human immunodeficiency virus type 1 Gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production. J. Virol. 85,305-314.
40. Robertson, D. L., and Joyce, G. F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467-468.
41. Romero-Lopez, C., Diaz-Gonzalez, R., Barroso-Deljesus, A., and Berzal-Herranz, A. (2009). Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule. J. Gen. Virol. 90, 1659-1669.
42. Rusconi, C. P., Scardino, E., Layzer, J., Pitoc, G. A., Ortel, T. L., Monroe, D., and Sullenger, B. A. (2002). RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419, 90-94.
43. Sun, W., Du, L., and Li, M. (2011). Advances and perspectives in cell-specific aptamers. Curr. Pharm. Des. 17,80-91.
44. Syed, M. A., and Pervaiz, S. (2010). Advances in aptamers. Oligonu-cleotides 20, 215-224.
45. Tian, Y., Adya, N., Wagner, S., Giam, C. Z., Green, M. R., and Ellington, A. D. (1995). Dissecting protein:protein interactions between transcription factors with an RNA aptamer. RNA 1,317-326.
46. Tuerk, C., and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
47. Tuerk, C., Macdougal, S., and Gold, L. (1992). RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. U.S.A. 89, 6988-6992.
48. Vuyisich, M., and Beal, P. A. (2002). Controlling protein activity with ligand-regulated RNA aptamers. Chem. Biol. 9, 907-913.
49. Wang, J., Jiang, H., and Liu, F. (2000). In vitro selection of novel RNA ligands that bind human cytomegalovirus and block viral infection. RNA 6, 571-583.
50. Wheeler, L. A., Trifonova, R., Vrbanac, V., Basar, E., Mckernan, S., Xu, Z., Seung, E., Deruaz, M., Dudek, T., Einarsson, J. I., Yang, L., Allen, T. M., Luster, A. D., Tager, A. M., Dykxhoorn, D. M., and Lieberman, J. (2011). Inhibition of HIV transmission in human cer-vicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras. J. Clin. Invest. 121, 2401-2412.
51. Zhou, J., Battig, M. R., and Wang, Y. (2010). Aptamer-based molecular recognition for biosensor development. Anal. Bioanal. Chem. 398, 2471-2480.
52. Zhou, J., Shu, Y., Guo, P., Smith, D. D., and Rossi, J. J. (2011). Dual functional RNA nanopar-ticles containing phi29 motor pRNA and anti-gp120 aptamer for cell-type specific delivery and HIV-1 inhibition. Methods 54, 284-294.