Skip to main content

Advertisement

Log in

Aptamers and riboswitches: perspectives in biotechnology

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Apte RS (2008) Pegaptanib sodium for the treatment of age-related macular degeneration. Expert Opin Pharmacother 9:499–508

    CAS  PubMed  Google Scholar 

  • Babendure JR, Adams SR, Tsien RY (2003) Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125:14716–14717

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR (2007) Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3:44–49

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497–500

    CAS  PubMed  Google Scholar 

  • Chen X, Li N, Ellington AD (2007) Ribozyme catalysis of metabolism in the RNA world. Chem Biodivers 4:633–655

    CAS  PubMed  Google Scholar 

  • Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9:2525–2531

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fowler CC, Brown ED, Li Y (2008) A FACS-based approach to engineering artificial riboswitches. ChemBioChem 9:1906–1911

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Hanson S, Berthelot K, Fink B, McCarthy JE, Suess B (2003) Tetracycline-aptamer-mediated translational regulation in yeast. Mol Microbiol 49:1627–1637

    CAS  PubMed  Google Scholar 

  • Harvey I, Garneau P, Pelletier J (2002) Inhibition of translation by RNA-small molecule interactions. RNA 8:452–463

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hermann T, Patel DJ (2000) Adaptive recognition by nucleic acid aptamers. Science 287:820–825

    CAS  PubMed  Google Scholar 

  • Holeman LA, Robinson SL, Szostak JW, Wilson C (1998) Isolation and characterization of fluorophore-binding RNA aptamers. Fold Des 3:423–431

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Huang CC, Chang HT (2008) Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem Commun (Camb) 12:1461–1463

    Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Kim DS, Gusti V, Pillai SG, Gaur RK (2005) An artificial riboswitch for controlling pre-mRNA splicing. RNA 11:1667–1677

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • 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)

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Levy M, Griswold KE, Ellington AD (2005) Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization. RNA 11:1555–1562

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Liss M, Petersen B, Wolf H, Prohaska E (2002) An aptamer-based quartz crystal protein biosensor. Anal Chem 74:4488–4495

    CAS  PubMed  Google Scholar 

  • Liu CW, Huang CC, Chang HT (2009) Highly selective DNA-based sensor for lead(II) and mercury(II) ions. Anal Chem 81:2383–2387

    CAS  PubMed  Google Scholar 

  • Lynch SA, Gallivan JP (2009) A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res 37:184–192

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mayer G (2009) The chemical biology of aptamers. Angew Chem Int Ed Engl 48:2672–2689

    CAS  PubMed  Google Scholar 

  • 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

    PubMed  PubMed Central  Google Scholar 

  • Nomura Y, Yokobayashi Y (2007) Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 129:13814–13815

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Serganov A, Huang L, Patel DJ (2008) Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455:1263–1267

    CAS  PubMed  PubMed Central  Google Scholar 

  • Serganov A, Huang L, Patel DJ (2009) Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature 458:233–237

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma V, Nomura Y, Yokobayashi Y (2008) Engineering complex riboswitch regulation by dual genetic selection. J Am Chem Soc 130:16310–16315

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Stadtherr K, Wolf H, Lindner P (2005) An aptamer-based protein biochip. Anal Chem 77:3437–3443

    CAS  PubMed  Google Scholar 

  • Strehlitz B, Nikolaus N, Stoltenburg R (2008) Protein detection with aptamer biosensors. Sensors 8:4296–4307

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Topp S, Gallivan JP (2008) Riboswitches in unexpected places–a synthetic riboswitch in a protein coding region. RNA 14:2498–2503

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Tyagi S (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat Methods 6:331–338

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Weigand JE, Suess B (2007) Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res 35:4179–4185

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Werstuck G, Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282:296–298

    CAS  PubMed  Google Scholar 

  • Wieland M, Hartig JS (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 47:2604–2607

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Wieland M, Gfell M, Hartig JS (2009b) Expanded hammerhead ribozymes containing addressable three-way junctions. RNA 15:968–976

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322:456–460

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Zaher HS, Unrau PJ (2007) Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 13:1017–1026

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

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

Authors

Corresponding author

Correspondence to Beatrix Suess.

Rights and permissions

Reprints 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

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-009-2194-2

Keywords

Navigation