Skip to main content
SpringerLink
Log in

Bioinformatic Analysis of the Contribution of Primer Sequences to Aptamer Structures

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

Aptamers are nucleic acid molecules selected in vitro to bind a particular ligand. While numerous experimental studies have examined the sequences, structures, and functions of individual aptamers, considerably fewer studies have applied bioinformatics approaches to try to infer more general principles from these individual studies. We have used a large Aptamer Database to parse the contributions of both random and constant regions to the secondary structures of more than 2000 aptamers. We find that the constant, primer-binding regions do not, in general, contribute significantly to aptamer structures. These results suggest that (a) binding function is not contributed to nor constrained by constant regions; (b) in consequence, the landscape of functional binding sequences is sparse but robust, favoring scenarios for short, functional nucleic acid sequences near origins; and (c) many pool designs for the selection of aptamers are likely to prove robust.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Ancel L, Fontana W (2000) Plasticity, modularity and evolvability in RNA in vitro. Exp Zool 288:242–283

    Article  CAS  Google Scholar 

  • Bartel DP, Szostak JW (1993) Isolation of new ribozymes from a large pool of random sequences. Science 261:1411–1417

    Article  PubMed  CAS  Google Scholar 

  • Carothers JM, Oestreich SC, Davis JH, Szostak JW (2004) Informational complexity and functional activity of RNA structures in vitro. Am Chem Soc 126:5130–5137

    Article  CAS  Google Scholar 

  • Coleman TM, Huang F (2002) RNA-catalyzed thioester synthesis. Chem Biol 9:1227–1236

    Article  PubMed  CAS  Google Scholar 

  • Coleman TM, Huang F (2005) Optimal random libraries for the isolation of catalytic RNA. RNA Biol 2:129–136

    PubMed  CAS  Google Scholar 

  • Connell GJ, Illangesekare M, Yarus M (1993) Three small ribooligonucleotides with specific arginine sites. Biochemistry 32:5497–5502

    Article  PubMed  CAS  Google Scholar 

  • Davidson EA, Ellington AD (2005) Engineering regulatory RNAs. Trends Biotechnol 23:109–112

    Article  PubMed  CAS  Google Scholar 

  • Dey AK, Griffiths C, Lea SM, James W (2005) Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA 11:873–884

    Article  PubMed  CAS  Google Scholar 

  • Doudna JA (2000) Structural genomics of RNA. Nature Struct Biol 7:954–956

    Article  PubMed  CAS  Google Scholar 

  • Ellington AD (1994) RNA selection. Aptamers achieve the desired recognition. Curr Biol 4:427–429

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Ellington AD, Khrapov M, Shaw CA (2000) The scene of a frozen accident. RNA 6:485–498

    Article  PubMed  CAS  Google Scholar 

  • Gevertz J, Gin HH, Schlick T (2005) In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11:853–863

    Article  PubMed  CAS  Google Scholar 

  • Hall B, Hesselberth JR, Ellington AD (2007) Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 22:1939–1947

    Article  Google Scholar 

  • Hofacker IF, Fontana W, Stadler BF, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatshefte Chemie 125:167–188

    Article  CAS  Google Scholar 

  • Huang Z, Szostak JW (2003) Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer. RNA 9:1456–1463

    Article  PubMed  CAS  Google Scholar 

  • Hughes RA, Robertson MP, Ellington AD, Levy M (2004) The importance of prebiotic chemistry in the RNA world. Curr Opin Chem Biol 8:629–633

    Article  PubMed  CAS  Google Scholar 

  • Isaacs FJ, Dwyer DJ, Collins JJ (2006) RNA synthetic biology. Nature Biotechnol 24:545–554

    Article  CAS  Google Scholar 

  • Jhaveri SD, Hirao I, Bell S, Uphoff KW, Ellington AD (1997) Landscapes for molecular evolution: lessons from in vitro selection experiments with nucleic acids. Annu Rep Comb Chem Mol Divers 1:169–191

    CAS  Google Scholar 

  • Joyce GF (2000) RNA structure: ribozyme evolution at the crossroads. Science 289:401–402

    Article  PubMed  CAS  Google Scholar 

  • Joyce GF (2004) Directed evolution of nucleic acid enzymes. Annu Rev Biochem 73:791–836

    Article  PubMed  CAS  Google Scholar 

  • Kim N, Gan HH, Schlick T (2007) A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA 13:478–492

    Article  PubMed  CAS  Google Scholar 

  • Knight R, Yarus M (2003) Analyzing partially randomized nucleic acid pools: straight dope on doping. Nucleic Acids Res 31:e30

    Article  PubMed  Google Scholar 

  • Lee JF, Hesselberth JR, Meyers LA, Ellington AD (2004) Aptamer Database. Nucleic Acids Res 32:D95–D100

    Article  PubMed  CAS  Google Scholar 

  • Lee JF, Stovall GM, Ellington AD (2006) Aptamer therapeutics advance. Curr Opin Chem Biol 10:282–289

    Article  PubMed  CAS  Google Scholar 

  • Legiewicz M, Lozupone C, Knight R, Yarus M (2005) Size, constant sequences, and optimal selection. RNA 11:1701–1709

    Article  PubMed  CAS  Google Scholar 

  • Lozupone C, Changayil S, Majerfeld I, Yarus M (2003) Selection of the simplest RNA that binds isoleucine. RNA 9:1315–1322

    Article  PubMed  CAS  Google Scholar 

  • Majerfeld I, Yarus M (1998) Isoleucine: RNA sites with associated coding sequences. RNA 4:471–478

    PubMed  CAS  Google Scholar 

  • Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure in vitro. Mol Biol 288:911–940

    Article  CAS  Google Scholar 

  • McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105–1109

    Article  PubMed  CAS  Google Scholar 

  • Meyers LA, Lee JF, Cowperthwaite MC, Ellington AD (2004) The robustness of naturally and artificially selected nucleic acid secondary structures in vitro. Mol Evol 58:618–625

    Google Scholar 

  • Patzel V (2004) In silico selection of functional RNA molecules. Curr Opin Drug Disc Dev 7:360–369

    CAS  Google Scholar 

  • Sabeti PC, Unrau PJ, Bartel DP (1997) Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem Biol 4:767–774

    Article  PubMed  CAS  Google Scholar 

  • Salehi-Ashtiani K, Szostak JW (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 414:82–84

    Article  PubMed  CAS  Google Scholar 

  • Sayer NM, Cubin M, Rhie A, Bullock M, Tahiri-Alaoui A, James W (2004) Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem 279:13102–13109

    Article  PubMed  CAS  Google Scholar 

  • Schultes EA, Bartel DP (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289:448–452

    Article  PubMed  CAS  Google Scholar 

  • Schuster P, Fontana W, Stadler P, Hofacker I (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc Roy Sci Lond B 255:279–284

    Article  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Ulrich H (2006) RNA aptamers: from basic science towards therapy. Handbk Exp Pharmacol 173:305–326

    Article  CAS  Google Scholar 

  • Wuchty S, Fontana W, Hofacker IL, Schuster P (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145–165

    Article  PubMed  CAS  Google Scholar 

  • Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244:48–52

    Article  PubMed  CAS  Google Scholar 

  • Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9:133–148

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA

    Matthew C. Cowperthwaite

  2. Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA

    Andrew D. Ellington

Authors
  1. Matthew C. Cowperthwaite
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew D. Ellington
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Matthew C. Cowperthwaite.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cowperthwaite, M.C., Ellington, A.D. Bioinformatic Analysis of the Contribution of Primer Sequences to Aptamer Structures. J Mol Evol 67, 95–102 (2008). https://doi.org/10.1007/s00239-008-9130-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-008-9130-4

Keywords

Search

Navigation