Abstract
Aptamers are short, single stranded nucleic acids which bind a wide range of different ligands with extraordinary high binding affinity and specificity. The steadily increasing number of aptamers is accompanied by an expanding range of applications in biotechnology. We will describe new developments in the field including the use of aptamers for conditional gene regulation and as biosensors. In addition, we will discuss the potential of aptamers as tags to visualize RNA and protein distribution in living cells and as therapeutics. Furthermore, we will consider biotechnological applications of riboswitches for gene regulation and as drug target.
Similar content being viewed by others
References
Adler A, Forster N, Homann M, Goringer HU (2008) Post-SELEX chemical optimization of a trypanosome-specific RNA aptamer. Comb Chem High Throughput Screen 11:16–23
An CI, Trinh VB, Yokobayashi Y (2006) Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 12:710–716
Apte RS (2008) Pegaptanib sodium for the treatment of age-related macular degeneration. Expert Opin Pharmacother 9:499–508
Babendure JR, Adams SR, Tsien RY (2003) Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125:14716–14717
Beisel CL, Bayer TS, Hoff KG, Smolke CD (2008) Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol 4:224
Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437–445
Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR (2007) Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3:44–49
Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, Li J, Liu N, Cao W, Zhu Y, Shen B, Shao N (2009) Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus. Nucleic Acids Res 37(14):4621–4628
Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497–500
Chen X, Li N, Ellington AD (2007) Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4:633–655
Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9:2525–2531
de-los Santos-Alvarez N, Lobo-Castanon MJ, Miranda-Ordieres AJ, Tunon-Blanco P (2007) Modified-RNA aptamer-based sensor for competitive impedimetric assay of neomycin B. J Am Chem Soc 129:3808–3809
Desai SK, Gallivan JP (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126:13247–13254
Ehrentreich-Forster E, Orgel D, Krause-Griep A, Cech B, Erdmann VA, Bier F, Scheller FW, Rimmele M (2008) Biosensor-based on-site explosives detection using aptamers as recognition elements. Anal Bioanal Chem 391:1793–1800
Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822
Eulberg D, Buchner K, Maasch C, Klussmann S (2005) Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res 33:e45
Eydeler K, Magbanua E, Werner A, Ziegelmuller P, Hahn U (2009) Fluorophore binding aptamers as a tool for RNA visualization. Biophys J 96:3703–3707
Fowler CC, Brown ED, Li Y (2008) A FACS-based approach to engineering artificial riboswitches. ChemBioChem 9:1906–1911
Grate D, Wilson C (2001) Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 9:2565–2570
Gusti V, Kim DS, Gaur RK (2008) Sequestering of the 3′ splice site in a theophylline-responsive riboswitch allows ligand-dependent control of alternative splicing. Oligonucleotides 18:93–99
Hafner M, Vianini E, Albertoni B, Marchetti L, Grune I, Gloeckner C, Famulok M (2008) Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization. Nat Protoc 3:579–587
Hanson S, Berthelot K, Fink B, McCarthy JE, Suess B (2003) Tetracycline-aptamer-mediated translational regulation in yeast. Mol Microbiol 49:1627–1637
Harvey I, Garneau P, Pelletier J (2002) Inhibition of translation by RNA-small molecule interactions. RNA 8:452–463
Hermann T, Patel DJ (2000) Adaptive recognition by nucleic acid aptamers. Science 287:820–825
Holeman LA, Robinson SL, Szostak JW, Wilson C (1998) Isolation and characterization of fluorophore-binding RNA aptamers. Fold Des 3:423–431
Homann M, Lorger M, Engstler M, Zacharias M, Goringer HU (2006) Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen 9:491–499
Huang CC, Chang HT (2008) Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem Commun (Camb) 12:1461–1463
Jo JJ, Shin JS (2009) Construction of intragenic synthetic riboswitches for detection of a small molecule. Biotechnol Lett. doi:https://doi.org/10.1007/s10529-009-0058-6
Kim DS, Gusti V, Pillai SG, Gaur RK (2005) An artificial riboswitch for controlling pre-mRNA splicing. RNA 11:1667–1677
Kim DS, Gusti V, Dery KJ, Gaur RK (2008) Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing. BMC Mol Biol 9:23
Kotter P, Weigand JE, Meyer B, Entian KD, Suess B (2009) A fast and efficient translational control system for conditional expression of yeast genes. Nucleic Acids Res. doi:https://doi.org/10.1093/nar/gkp578
Lee ER, Blount KF, Breaker RR (2009a) Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol 6(2)
Lee HJ, Kim BC, Kim KW, Kim YK, Kim J, Oh MK (2009b) A sensitive method to detect Escherichia coli based on immunomagnetic separation and real-time PCR amplification of aptamers. Biosens Bioelectron 24(12):3550–3555
Levy M, Griswold KE, Ellington AD (2005) Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. RNA 11:1555–1562
Li W, Yang X, Wang K, Tan W, He Y, Guo Q, Tang H, Liu J (2008) Real-time imaging of protein internalization using aptamer conjugates. Anal Chem 80:5002–5008
Liss M, Petersen B, Wolf H, Prohaska E (2002) An aptamer-based quartz crystal protein biosensor. Anal Chem 74:4488–4495
Liu CW, Huang CC, Chang HT (2009) Highly selective DNA-based sensor for lead(II) and mercury(II) ions. Anal Chem 81:2383–2387
Lynch SA, Gallivan JP (2009) A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 37:184–192
Lynch SA, Desai SK, Sajja HK, Gallivan JP (2007) A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol 14:173–184
Mayer G (2009) The chemical biology of aptamers. Angew Chem Int Ed Engl 48:2672–2689
Muranaka N, Sharma V, Nomura Y, Yokobayashi Y (2009) An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res 37:e39
Nomura Y, Yokobayashi Y (2007) Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 129:13814–13815
Ott E, Stolz J, Lehmann M, Mack M (2009) The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis. RNA Biol 6
Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305–334
Sando S, Narita A, Aoyama Y (2007) Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. ChemBioChem 8:1795–1803
Serganov A, Huang L, Patel DJ (2008) Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455:1263–1267
Serganov A, Huang L, Patel DJ (2009) Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458:233–237
Sharma V, Nomura Y, Yokobayashi Y (2008) Engineering complex riboswitch regulation by dual genetic selection. J Am Chem Soc 130:16310–16315
Sparano BA, Koide K (2007) Fluorescent sensors for specific RNA: a general paradigm using chemistry and combinatorial biology. J Am Chem Soc 129:4785–4794
Stadtherr K, Wolf H, Lindner P (2005) An aptamer-based protein biochip. Anal Chem 77:3437–3443
Strehlitz B, Nikolaus N, Stoltenburg R (2008) Protein detection with aptamer biosensors. Sensors 8:4296–4307
Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR (2005) Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol 12:1325–1335
Suess B, Hanson S, Berens C, Fink B, Schroeder R, Hillen W (2003) Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res 31:1853–1858
Suess B, Fink B, Berens C, Stentz R, Hillen W (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 32:1610–1614
Swensen JS, Xiao Y, Ferguson BS, Lubin AA, Lai RY, Heeger AJ, Plaxco KW, Soh HT (2009) Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic, electrochemical aptamer-based sensor. J Am Chem Soc 131:4262–4266
Thore S, Frick C, Ban N (2008) Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. J Am Chem Soc 130:8116–8117
Topp S, Gallivan JP (2008) Riboswitches in unexpected places–a synthetic riboswitch in a protein coding region. RNA 14:2498–2503
Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510
Tuleuova N, An CI, Ramanculov E, Revzin A, Yokobayashi Y (2008) Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction. Biochem Biophys Res Commun 376:169–173
Tyagi S (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat Methods 6:331–338
Valencia-Burton M, McCullough RM, Cantor CR, Broude NE (2007) RNA visualization in live bacterial cells using fluorescent protein complementation. Nat Methods 4:421–427
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR (2007) Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19:3437–3450
Weigand JE, Suess B (2007) Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res 35:4179–4185
Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B (2008) Screening for engineered neomycin riboswitches that control translation initiation. RNA 14:89–97
Werstuck G, Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296–298
Wieland M, Hartig JS (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 47:2604–2607
Wieland M, Benz A, Klauser B, Hartig JS (2009a) Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl 48:2715–2718
Wieland M, Gfell M, Hartig JS (2009b) Expanded hammerhead ribozymes containing addressable three-way junctions. RNA 15:968–976
Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 104:14283–14288
Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322:456–460
Wochner A, Cech B, Menger M, Erdmann VA, Glokler J (2007) Semi-automated selection of DNA aptamers using magnetic particle handling. Biotechniques 43:344–344, 346, 348 passim
Yamazaki S, Tan L, Mayer G, Hartig JS, Song JN, Reuter S, Restle T, Laufer SD, Grohmann D, Krausslich HG, Bajorath J, Famulok M (2007) Aptamer displacement identifies alternative small-molecule target sites that escape viral resistance. Chem Biol 14:804–812
Zaher HS, Unrau PJ (2007) Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 13:1017–1026
Acknowledgment
We thank Jens Wöhnert for the critical reading of the manuscript. We are grateful to the Aventis Foundation and the Deutsche Forschungsgemeinschaft for their financial support.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Weigand, J.E., Suess, B. Aptamers and riboswitches: perspectives in biotechnology. Appl Microbiol Biotechnol 85, 229–236 (2009). https://doi.org/10.1007/s00253-009-2194-2
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-009-2194-2