Aptamers targeting RNA molecules

Methods in Molecular Biology

Volumn 535, Issue , 2009, Pages 79-105

  Watrin, Marguerite ^a,b   Dausse, Eric ^a,b   Lebars, Isabelle ^b   Rayner, Bernard ^a,b   Bugaut, Anthony ^a,b   Toulmé, Jean Jacques ^a,b  

^a INSTITUT EUROPÉEN DE CHIMIE ET BIOLOGIE   (France)

^b UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

dynamic combinatorial chemistry; genomic SELEX; hairpins; NMR structure; RNA structures; TAR RNA

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

APTAMER; RNA;

ARTICLE; CHEMISTRY; COMBINATORIAL CHEMISTRY; CONFORMATION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INVERTED REPEAT; LONG TERMINAL REPEAT; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE;

APTAMERS, NUCLEOTIDE; COMBINATORIAL CHEMISTRY TECHNIQUES; HIV LONG TERMINAL REPEAT; HIV-1; HUMANS; INVERTED REPEAT SEQUENCES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA; SELEX APTAMER TECHNIQUE;

EID: 77749233318     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-557-2_6     Document Type: Article

References (61)

1. Osborne, S.E. and Ellington, A.E. (1997) Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349-370. (Pubitemid 127659248)
2. Toulmé, J.J., Di Primo, C. and Boucard, D. (2004) Regulating eukaryotic gene expression with aptamers. FEBS Lett. 567, 55-62. (Pubitemid 38686423)
3. Nimjee, S.M., Rusconi, C.P. and Sullenger, B.A. (2005) Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56, 555-583. (Pubitemid 40299797)
4. Toulmé, J.-J., Di Primo, C. and Moreau, S. (2001) Modulation of RNA function by oli-gonucleotides recognizing RNA structure. Progr. Nucleic Acid Res. Mol. Biol. 69, 1-46. (Pubitemid 33804675)
5. Soukup, G.A., Ellington, A.D. and Maher, L.J. (1996) Selection of RNAs that bind to duplex DNA at neutral pH. J. Mol. Biol. 259, 216-228. (Pubitemid 26176026)
6. Ducongé, F. and Toulmé, 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.
7. Boiziau, C., Dausse, E., Yurchenko, L. and Toulmé, J.J. (1999) DNA aptamers selected against the HIV-1 TAR RNA element form RNA/DNA kissing complexes. J. Biol. Chem. 274, 12730-12737.
8. 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. (Pubitemid 40360998)
9. Shao, Y., Chan, C.Y., Maliyekkel, A., Lawrence, C.E., Roninson, I.B. and Ding, Y. (2007) Effect of target secondary structure on RNAi efficiency. RNA 13, 1631-1640. (Pubitemid 47481671)
10. Yoshinari, K., Miyagishi, M. and Taira, K. (2004) Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res. 32, 691-699. (Pubitemid 38263060)
11. Darfeuille, F., Reigadas, S., Hansen, J.B., Orum, H., Di Primo, C. and Toulme, J.J. (2006) Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides. Biochemistry 45, 12076-12082. (Pubitemid 44497833)
12. Scarabino, D., Crisari, A., Lorenzini, S., Williams, K. and Tocchini-Valentini, G.P. (1999) tRNA prefers to kiss. EMBO J. 18, 4571-4578. (Pubitemid 29391266)
13. Aldaz-Carroll, L., Tallet, B., Dausse, E., Yurchenko, L. and Toulmé, 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. (Pubitemid 34462709)
14. 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. Commun. 322, 820-826. (Pubitemid 39164426)
15. Tomizawa, J.I. (1990) Control of ColE1 plasmid replication: intermediates in the binding of RNA I and RNA II. J. Mol. Biol. 212, 683-694.
16. Ferrandon, D., Koch, I., Westof, E. and Nusslein-Volhard, C. (1997) RNA-RNA interaction is required for the formation of specific bicoid mRNA 3'UTR-STAUFEN ribonucleoproteic particles. EMBO J. 16, 1751-1758. (Pubitemid 27161638)
17. Kolb, G., Reigadas, S., Castanotto, D., Faure, A., Ventura, M., Rossi, J.J. and Toulme, J.J. (2006) Endogenous expression of ananti-TAR aptamer reduces HIV-1 replication. RNA Biol. 3, 150-156. (Pubitemid 46495343)
18. Darfeuille, F., Arzumanov, A., Gait, M.J., Di Primo, C. and Toulmé, J.-J. (2002) 2'-O-methyl-RNA hairpins generate loop-loop complexes and selectively inhibit HIV-1 Tat-mediated transcription. Biochemistry 41, 12186-12192.
19. Darfeuille, F., Arzumanov, A., Gryaznov, S., Gait, M.J., Di Primo, C. and Toulmé, J.J. (2002) Loop-loop interaction of HIV-1 TAR RNA with N3'->P5' deoxyphosphor-amidate aptamers inhibits in vitro Tat-mediated transcription. Proc. Natl. Acad. Sci. U.S.A. 99, 9709-9714. (Pubitemid 34831112)
20. Darfeuille, F., Hansen, J.B., Orum, H., Di Primo, C. and Toulmé, 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. (Pubitemid 39023001)
21. Kolb, G., Reigadas, S., Boiziau, C., Van Aer-schot, A., Arzumanov, A., Gait, M., Herde-wijn, P. and Toulmé, J.J. (2005) Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 44, 2926-2933. (Pubitemid 40293667)
22. Dausse, E., Cazenave, C., Rayner, B. and Toulmé, J.J. (2005) In vitro selection procedures for identifying DNA and RNA apta-mers targeted to nucleic acids and proteins. Methods Mol. Biol. 288, 391-410.
23. Corbett, P.T., Leclaire, J., Vial, L., West, K.R., Wietor, J.L., Sanders, J.K. and Otto, S. (2006) Dynamic combinatorial chemistry. Chem. Rev. 106, 3652-3711. (Pubitemid 44565983)
24. Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligor-ibonucleotide synthesis using T7 RNA poly-merase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798.
25. Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck O.C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol., 180, 51-62. (Pubitemid 20039565)
26. Wyatt, J.R., Chastain, M. and Puglisi, J.D. (1991) Synthesis and purification of large amounts of RNA oligonucleotides. BioTech-niques 11, 764-769.
27. Gold, L., Brown, D., He, Y., Shtatland, T., Singer, B.S. and Wu, Y. (1997) From oligo-nucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc. Natl. Acad. Sci. U.S.A. 94, 59-64. (Pubitemid 27031017)
28. Lorenz, C., von Pelchrzim, F. and Schroe-der, R. (2006) Genomic systematic evolution of ligands by exponential enrichment (Genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels. Nat. Protoc. 1, 2204-2212.
29. Singer, B.S., Shtatland, T., Brown, D. and Gold, L. (1997) Libraries for genomic SELEX. Nucleic Acids Res. 25, 781-786. (Pubitemid 27299833)
30. Bannwarth, S. and Gatignol, A. (2005) HIV-1 TAR RNA: the target of molecular interactions between the virus and its host. Curr. HIV Res. 3, 61-71. (Pubitemid 40081286)
31. Gold, L., Brown, D., He, Y.Y., Shtatland, T., Singer, B.S. and Wu, Y. (1997) From oligo-nucleotide shapes to genomic SELEX: Novel biological regulatory loops. Proc. Natl. Acad. Sci. U.S.A. 94, 59-64. (Pubitemid 27031017)
32. Darfeuille, F., Sekkai, D., Dausse, E., Kolb, G., Yurchenko, L., Boiziau, C. and Toulmé, J.-J. (2002) Driving in vitro selection of anti-HIV-1 TAR aptamersbymagnesium concentration and temperature. Combinat. Chem. High Throughput Screening 5, 315-327.
33. Pieles, U., Zurcher, W., Schar, M. and Moser, H.E. (1993) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for the mass and sequence analysis of natural and modified oligonucleotides. Nucleic Acids Res. 21, 3191-3196. (Pubitemid 23230487)
34. Bugaut, A., Bathany, K., Schmitter, J.M. and Rayner, B. (2005) Target-induced selection of ligands from a dynamic combinatorial library of mono-and bi-conjugated oligonu-cleotides. Tetrahedron Lett. 46, 687-690. (Pubitemid 40037930)
35. Varani, G. and Tinoco, I. Jr. (1991) RNA structure and NMR spectroscopy. Q. Rev. Biophys., 24, 479-532. (Pubitemid 21916777)
36. Varani, G., Aboul-ela, F. and Allain, F.H.-T. (1996) NMR investigation of RNA structure. Prog Nucl. Magn. Reso. Spectrosc., 29, 51-127. (Pubitemid 126381972)
37. Fürtig, B., Richter, C., Wöhnert, J. and Schwalbe, H. (2003) NMR Spectroscopy of RNA. ChemBioChem., 4, 936-962. (Pubitemid 37267582)
38. Latham, M.P., Brown, D.J., McCallum, S.A. and Pardi A. (2005) NMR methods for studying the structure and dynamics of RNA. ChemBioChem., 6, 1492-1505. (Pubitemid 41296958)
39. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley, New York.
40. Wüthrich, K. (1989) Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science 243, 45-50. (Pubitemid 19027923)
41. Usman, N., Ogilvie, K.K., Jiang, M.-Y. and Cedergren, R.J. (1987) Automated chemical synthesis of long oligonucleotides using 2'-O-silylated ribonucleoside 3'-O-phosphora-midites on a controlled-pore glass support: Synthesis of a 43-nucleotide sequence similar to the 3'-half molecule of an Escherichia coli formylmethionine tRNA. J.Am.Chem.Soc. 109, 7845-7854. (Pubitemid 18011363)
42. Ogilvie, K.K., Usman, N., Nicoghosian, K. and Cedergren, R.J. (1988) Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity. Proc.Natl.Acad. Sci. U.S.A. 85, 5764-5768.
43. Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Swee-dler, D., Gonzalez, C. et al. (1995) Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res. 23, 2677-2684.
44. Kao, C., Rüdisser, S. and Zheng, M. (2001) A simple and efficient method to transcribe RNAs with reduced 3' heterogeneity. Methods 23, 201-205. (Pubitemid 32848420)
45. Lapham, J. and Crothers, D.M. (1996) RNase H cleavage fpr processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA, 2, 289-296. (Pubitemid 26371298)
46. Grosshans, C.A. and Cech, T.R. (1991) A hammerhead ribozyme allows synthesis of a new form of the Tetrahymena ribozyme homogeneous in length with a 3' end blocked for transesterification. Nucleic Acids Res. 19, 3875-3880. (Pubitemid 21912755)
47. Ferre-D'Amare, A.R. and Doudna, J.A. (1996) Use of cis-and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed rna. Nucleic Acids Res. 24, 977-978.
48. Bodenhausen, G. and Ruben, D.J. (1980) Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem. Phys. Lett. 69, 185.
49. Braunschweiler, L. and Ernst, R.R. (1983) Coherence transfer by isotropic mixing: application to proton correlation spectro-scopy. J. Magn. Reson. 53, 521.
50. Bax, A. and Davis, D.G. (1985) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65, 355-360.
51. Piantini, U., Sorensen, O.W. and Ernst, R.R. (1982) Multiple quantum filters for elucidating NMR coupling networks. J. Am. Chem. Soc., 104, 6800-6801.
52. 13C-enriched proteins. J. Magn. Reson. 88, 425-431.
53. 13C Magnetization transfer by isotropic mixing. spin system identification in large proteins. J. Am. Chem. Soc. 112, 886-888. (Pubitemid 20093846)
54. Kay, L.E., Marion, D. and Bax, A. (1989) Practical aspects of three-dimensional het-eronuclear NMR of proteins. J. Magn.Reson. 84, 72-84.
55. 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Lett., 208, 94-98.
56. 31P triple resonance experiment: HCP-CCH-TOCSY. J. Biomol. NMR 5, 87-92.
57. Brünger, A.T. (1990) X-PLOR Manual. Yale University, New Haven, CT.
58. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simon-son, T. and Warren, G.L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D. Biol. Crystallogr. 54, 905-921.
59. Henning, M. and Williamson; J.R. (2000) Detection of N-H..N hydrogen bonding in RNA via scalar couplings in the absence of observable imino proton resonances. Nucleic Acids Res. 28, 1585-1593. (Pubitemid 30160571)
60. Dingley, A.J. and Grzesiek, S. (1998) Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide 2JNN Couplings. J. Am. Chem. Soc. 120, 8294-8297.
61. van Dongen, M.J.P., Wijmenga, S.S., Eritja, R., Azorin, F. and Hilbers, C.W. (1996) Through-bond correlation of adenine H2 and H8 protons in unlabeled DNA by HMBC spectroscopy. J.Biomol.NMR 8, 207-212. (Pubitemid 126706789)