Abstract
Functional nucleic acids such as aptamers and allosteric ribozymes can sense their ligands specifically, thereby undergoing structural alterations that can be converted into a detectable signal. The direct coupling of molecular recognition to signal generation in real time allows the generation of versatile reporters that can be applied in high-throughput screening (HTS). In the following chapter we describe different types of nucleic acids that have been applied successfully in screening approaches. We first refer to DNA and RNA aptamers, then consider allosteric ribozymes, and finally present examples of natural nucleic acids that were applied in screening assays.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Owicki, J.C. (2000) Fluorescence polarization and anisotropy in high throughput screening: perspectives and primer. J. Biomol. Screen. 5:297–306.
Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature (Lond.) 346:818–822.
Robertson, D.L. and Joyce, G.F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature (Lond.) 344:467–468.
Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510.
Famulok, M. (2005) Allosteric aptamers and aptazymes as probes for screening approaches. Curr. Opin. Mol. Ther. 7:137–143.
Silverman, S.K. (2003) Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9:377–383.
Roth, A. and Breaker, R.R. (2004) Selection in vitro of allosteric ribozymes. Methods Mol. Biol. 252:145–164.
Breaker, R.R. (2002) Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13:31–39.
Winkler, W.C. and Breaker, R.R. (2003) Genetic control by metabolite-binding riboswitches. ChemBioChem 4:1024–1032.
Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., Wickiser, J.K. and Breaker, R.R. (2004) New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. USA 101:6421–6426.
Yang, Y., Kochoyan, M., Burgstaller, P., Westhof, E. and Famulok, M. (1996) Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272:1343–1347.
Williamson, J.R. (2000) Induced fit in RNA–protein recognition. Nat. Struct. Biol. 7:834–837.
Nutiu, R. and Li, Y. (2003) Structure-switching signaling aptamers. J. Am. Chem. Soc. 125:4771–4778.
Nutiu, R., Yu, J.M.Y. and Li, Y. (2004) Signaling aptamers for monitoring enzymatic activity and for inhibitor screening. ChemBioChem 5:1139–1144.
Elowe, N.H., Nutiu, R., Allali-Hassani, A., Cechetto, J.D., Hughes, D.W., Li, Y. and Brown, E.D. (2006) Small-molecule screening made simple for a difficult target with a signaling nucleic acid aptamer that reports on deaminase activity. Angew. Chem. Int. Ed. Engl. 45:5648–5652.
Hafner, M., Schmitz, A., Grune, I., Srivatsan, S.G., Paul, B., Kolanus, W., Quast, T., Kremmer, E., Bauer, I. and Famulok, M. (2006) Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance. Nature (Lond.) 444:941–944.
Tang, J. and Breaker, R.R. (1997) Rational design of allosteric ribozymes. Chem. Biol. 4:453–459.
Najafi-Shoushtari, S.H., Mayer, G. and Famulok, M. (2004) Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res. 32:3212–3219.
Piganeau, N., Thuillier, V. and Famulok, M. (2001) In vitro selection of allosteric ribozymes: theory and experimental validation. J. Mol. Biol. 312:1177–1190.
Piganeau, N., Jenne, A., Thuillier, V. and Famulok, M. (2001) An allosteric ribozyme regulated by doxycyline. Angew. Chem. Int. Ed. Engl. 40:3503.
Koizumi, M., Soukup, G.A., Kerr, J.N. and Breaker, R.R. (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat. Struct. Biol. 6:1062–1071.
Robertson, M.P. and Ellington, A.D. (2001) In vitro selection of nucleoprotein enzymes. Nat. Biotechnol. 19:650–655.
Robertson, M.P., Knudsen, S.M. and Ellington, A.D. (2004) In vitro selection of ribozymes dependent on peptides for activity. RNA 10:114–127.
Soukup, G.A. and Breaker, R.R. (1999) Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA 96:3584–3589.
Srinivasan, J., Cload, S.T., Hamaguchi, N., Kurz, J., Keene, S., Kurz, M., Boomer, R.M., Blanchard, J., Epstein, D., Wilson, C. and Diener, J.L. (2004) ADP-specific sensors enable universal assay of protein kinase activity. Chem. Biol. 11:499–508.
Hartig, J.S., Najafi-Shoushtari, S.H., Grune, I., Yan, A., Ellington, A.D. and Famulok, M. (2002) Protein-dependent ribozymes report molecular interactions in real time. Nat. Bio-technol. 20:717–722.
Hartig, J.S. and Famulok, M. (2002) Reporter ribozymes for real-time analysis of domain-specific interactions in biomolecules: HIV-1 reverse transcriptase and the primer-template complex. Angew. Chem. Int. Ed. Engl. 41:4263–4266.
Najafi-Shoushtari, S.H. and Famulok, M. (2007) DNA aptamer-mediated regulation of the hairpin ribozyme by human alpha-thrombin. Blood Cells Mol. Dis. 38:19–24.
Winkler, W.C. (2005) Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr. Opin. Chem. Biol. 9:594–602.
Blount, K. and Breaker, R. (2006) Riboswitches as antibacterial drug targets. Nat. Biotechnol. 12:1558–1564.
Mayer, G. and Famulok, M. (2006) High-throughput-compatible assay for glmS riboswitch metabolite dependence. ChemBioChem 7:602–604.
Blount, K., Puskarz, I., Penchovsky, R. and Breaker, R. (2006) Development and application of a high-throughput assay for glmS riboswitch activators. RNA Biol. 3:77–81.
Sudarsan, N., Wickiser, J.K., Nakamura, S., Ebert, M.S. and Breaker, R.R. (2003) An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17:2688–2697.
Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G.M. and Breaker, R.R. (2005) Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithia-mine. Chem. Biol. 12:1325–1335.
Davies, B.P. and Arenz, C. (2006) A homogenous assay for micro RNA maturation. Angew. Chem. Int. Ed. Engl. 45:5550–5552.
Acknowledgments
We thank the DFG, the SFBs 645 and 704 for grants to M.F., and the Austrian Academy of Sciences for a grant to A.R. and the members of the Famulok lab. This work was supported by Aventis Gencell and by a grant from the Volkswagen Foundation (Priority program “conformational control”) to M.F. We thank M. Blind, G. Mayer, D. Proske, and G. Sengle (Universitat Bonn) for helpful discussions as well as J. Crouzet, J.F. Mayaux, and M. Finer (Aventis Gencell) for support.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Rentmeister, A., Famulok, M. (2009). Functional Nucleic Acid Sensors as Screening Tools. In: Yingfu, L., Yi, L. (eds) Functional Nucleic Acids for Analytical Applications. Integrated Analytical Systems. Springer, New York, NY. https://doi.org/10.1007/978-0-387-73711-9_13
Download citation
DOI: https://doi.org/10.1007/978-0-387-73711-9_13
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-73710-2
Online ISBN: 978-0-387-73711-9
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)