SpringerProtocols: Abstract: Aptamers Targeting RNA Molecules

6. Aptamers Targeting RNA Molecules

By: Marguerite Watrin², Eric Dausse², Isabelle Lebars³, Bernard Rayner², Anthony Bugaut², Jean-Jacques Toulmé²

Abstract

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Oligonucleotides complementary to RNA sequences interact poorly with folded target regions. In vitro selection of oligonucleotides carried out against RNA structures have led to aptamers that frequently differ from antisense sequences, but rather take advantage of non-double-stranded peculiarities of the target. Studies along this line provide information about tertiary RNA architectures as well as their interaction with ligand of interest. We describe here a genomic SELEX approach and its application to the recognition of stem–loop structures prone to the formation of kissing complexes. We also provide technical details for running a procedure termed 2D-SELEX that takes advantage of both in vitro selection and dynamic combinatorial chemistry. This allows selecting aptamer derivatives containing modified nucleotides that cannot be incorporated by polymerases. Last we present in vitro transcription conditions under which large amounts of RNA, suitable for NMR structural studies, can be obtained. These different aspects of the SELEX technology have been applied to the trans-activating responsive element of the human immunodeficiency virus type 1, which is crucial for the transcription of the retroviral genome.

Affiliation(s): (2) INSERM, Institut Européen de Chimie et Biologie, Pessac, France, Université Victor Segalen, Bordeaux, France
(3) CNRS – Université Bordeaux, Institut Européen de Chimie et Biologie, Pessac, France

Book Title: Nucleic Acid and Peptide Aptamers: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 535 | Pub. Date: Mar-03-2009 | Page Range: 1-27 | DOI: 10.1007/978-1-59745-557-2_6

Subject: Cell Biology

Key Words: RNA structures - hairpins - TAR RNA - genomic SELEX - dynamic combinatorial chemistry - NMR structure

References

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1.	Osborne, S.E. and Ellington, A.E. (1997) Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349–370.

2.	Toulmé, J.J., Di Primo, C. and Boucard, D. (2004) Regulating eukaryotic gene expression with aptamers. FEBS Lett. 567, 55–62.

3.	Nimjee, S.M., Rusconi, C.P. and Sullenger, B.A. (2005) Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56, 555–583.

4.	Toulmé, J.-J., Di Primo, C. and Moreau, S. (2001) Modulation of RNA function by oligonucleotides recognizing RNA structure. Progr. Nucleic Acid Res. Mol. Biol. 69, 1–46.

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.

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.

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.

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.

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.

12.	Scarabino, D., Crisari, A., Lorenzini, S., Williams, K. and Tocchini-Valentini, G.P. (1999) tRNA prefers to kiss. EMBO J. 18, 4571–4578.

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.

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.

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.

17.	Kolb, G., Reigadas, S., Castanotto, D., Faure, A., Ventura, M., Rossi, J.J. and Toulme, J.J. (2006) Endogenous expression of an anti-TAR aptamer reduces HIV-1 replication. RNA Biol. 3, 150–156.

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' deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription. Proc. Natl. Acad. Sci. U.S.A. 99, 9709–9714.

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.

21.	Kolb, G., Reigadas, S., Boiziau, C., Van Aerschot, A., Arzumanov, A., Gait, M., Herdewijn, P. and Toulmé, J.J. (2005) Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 44, 2926–2933.

22.	Dausse, E., Cazenave, C., Rayner, B. and Toulmé, J.J. (2005) In vitro selection procedures for identifying DNA and RNA aptamers 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.

24.	Milligan, J.F., Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase 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.

26.	Wyatt, J.R., Chastain, M. and Puglisi, J.D. (1991) Synthesis and purification of large amounts of RNA oligonucleotides. BioTechniques 11, 764–769.

27.	Gold, L., Brown, D., He, Y., Shtatland, T., Singer, B.S. and Wu, Y. (1997) From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc. Natl. Acad. Sci. U.S.A. 94, 59–64.

28.	Lorenz, C., von Pelchrzim, F. and Schroeder, 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.

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.

31.	Gold, L., Brown, D., He, Y.Y., Shtatland, T., Singer, B.S. and Wu, Y. (1997) From oligonucleotide shapes to genomic SELEX: Novel biological regulatory loops. Proc. Natl. Acad. Sci. U.S.A. 94, 59–64.

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 aptamers by magnesium 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.

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 oligonucleotides. Tetrahedron Lett. 46, 687–690.

35.	Varani, G. and Tinoco, I. Jr. (1991) RNA structure and NMR spectroscopy. Q. Rev. Biophys., 24, 479–532.

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.

37.	Fürtig, B., Richter, C., Wöhnert, J. and Schwalbe, H. (2003) NMR Spectroscopy of RNA. ChemBioChem., 4, 936–962.

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.

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.

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-phosphoramidites 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.

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., Sweedler, 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.

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.

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.

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 spectroscopy. 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.	Bax, A., Clore, G.M. and Gronenborn, A.M. (1990) ¹H-¹H correlation via isotropic mixing of ¹³C magnetization: a new three-dimensional approach for assigning ¹H and ¹³C spectra of ¹³C-enriched proteins. J. Magn. Reson. 88, 425–431.

53.	Fesik, S.W., Eaton, H.L., Olejniczak, E.T. and Zuiderweg, E.R.P. (1990) 2D and 3D NMR Spectroscopy Employing ¹³C-¹³C Magnetization transfer by isotropic mixing. spin system identification in large proteins. J. Am. Chem. Soc. 112, 886–888.

54.	Kay, L.E., Marion, D. and Bax, A. (1989) Practical aspects of three-dimensional heteronuclear NMR of proteins. J. Magn.Reson. 84, 72–84.

55.	Sklenar, V., Miyashiro, H., Zon, G., Miles, H.T. and Bax, A. (1986) Assignment of ³¹P and ¹H resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Lett., 208, 94–98.

56.	Marino, J.P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D.M. and Griesinger, C. (1995) Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by ¹H, ¹³C, 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., Simonson, 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.

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.

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