Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA

Nature Chemistry volume 3, pages 603–608 (2011)Cite this article

Subjects

Abstract

The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Enzyme-free primer extension.
Figure 2: Immobilization favours quantitative incorporation of nucleotides.
Figure 3: Sequential extension of a primer by any of the four different ribonucleotides.
Figure 4: Sequence selectivity of primer extension, as determined by assays with mixtures of all four monomers.
Figure 5: Rapid microhelper-free incorporation of two subsequent nucleotides on template 5 that can loop back to form a hairpin.

References

  1. Lilley, D. M. J. & Eckstein, F. Ribozymes and RNA Catalysis (RSC Publishing, 2008).

  2. Benner, S. A., Burgstaller, P., Battersby, T. R. & Jurczyk, S. in The RNA World 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 163–181 (Cold Spring Harbor Laboratory Press, 1999).

  3. Eschenmoser, A. Chemical etiology of nucleic acid structure. Science 284, 2118–2124 (1999).

    Article  CAS  Google Scholar 

  4. Ferris, J. P. Montmorillonite catalysis of 30–50 mer oligonucleotides: laboratory demonstration of potential steps in the origin of the RNA world. Origins Life Evol. Bios. 32, 311–332 (2002).

    Article  CAS  Google Scholar 

  5. Huang, W. & Ferris, J. P. One-step, regioselective synthesis of up to 50-mers of RNA oligomers by montmorillonite catalysis. J. Am. Chem. Soc. 128, 8914–8919 (2006).

    Article  CAS  Google Scholar 

  6. Orgel, L. E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 39, 99–123 (2004).

    Article  CAS  Google Scholar 

  7. Orgel, L. E. in The RNA World 3rd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 23–56 (Cold Spring Harbor Laboratory Press, 2006).

  8. Hill, A. R. Jr, Wu, T. & Orgel, L. E. The limits of template-directed synthesis with nucleoside-5′-phosphoro(2-methyl)imidazolides. Origins of Life Evol. Bios. 23, 285–290 (1993).

    Article  CAS  Google Scholar 

  9. Wu, T. & Orgel, L. E. Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides. J. Am. Chem. Soc. 114, 317–322 (1992).

    Article  CAS  Google Scholar 

  10. Vogel, S. R., Deck, C. & Richert, C. Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements. Chem. Commun. 4922–4924 (2005).

  11. Hartel, C. & Göbel, M. W. Substitution of adenine by purine-2,6-diamine improves the nonenzymatic oligomerization of ribonucleotides on templates containing thymidine. Helv. Chim. Acta 83, 2541–2549 (2000).

    Article  CAS  Google Scholar 

  12. Schrum, J. P., Ricardo, A., Krishnamurthy, M., Blain, J. C. & Szostak, J. W. Efficient and rapid template-directed nucleic acid copying using 2′-amino-2′,3′-dideoxyribonucleoside-5′-phosphorimidazolide monomers. J. Am. Chem. Soc. 131, 14560–14570 (2009).

    Article  CAS  Google Scholar 

  13. Hey, M., Hartel, C. & Göbel, M. W. Nonenzymatic oligomerization of ribonucleotides: towards in vitro selection experiments. Helv. Chim. Acta 86, 844–854 (2003).

    Article  CAS  Google Scholar 

  14. Kozlov, I. A. et al. Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure. J. Am. Chem. Soc. 121, 2653–2656 (1999).

    Article  CAS  Google Scholar 

  15. Mansy, S. S. et al. Template-directed synthesis of a genetic polymer in a model protocell. Nature 454, 122–125 (2008).

    Article  CAS  Google Scholar 

  16. Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E. & Bartel, D. P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292, 1319–1325 (2001).

    Article  CAS  Google Scholar 

  17. Vogel, S. R. & Richert, C. Adenosine residues in the template do not block spontaneous replication steps of RNA. Chem. Commun. 1896–1898 (2007).

  18. Inoue, T. & Orgel, L. E. Substituent control of the poly (C)-directed oligomerization of guanosine 5′-phosphoroimidazolide. J. Am. Chem. Soc. 103, 7666–7667 (1981).

    Article  CAS  Google Scholar 

  19. Kervio, E., Hochgesand, A., Steiner U. & Richert, C. Templating efficiency of naked DNA. Proc. Natl Acad. Sci. USA 107, 12074–12079 (2010).

    Article  CAS  Google Scholar 

  20. Rajamani, S. J. et al. Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J. Am. Chem. Soc. 132, 5880–5885 (2010).

    Article  CAS  Google Scholar 

  21. Kanavarioti, A., Bernasconi, C. F. & Baird, E. E. Effects of monomer and template concentration on the kinetics of nonenzymatic template-directed oligoguanylate synthesis. J. Am. Chem. Soc. 120, 8575–8581 (1998).

    Article  CAS  Google Scholar 

  22. Von Kiedrowski, G., Wlotzka, B., Helbing, J., Matzen, M. & Jordan, S. Parabolic growth of a self-replicating hexadeoxynucleotide bearing a 3′–5′-phosphate linkage. Angew. Chem. Int. Ed. Engl. 30, 423–426 (1991).

    Article  Google Scholar 

  23. Luther, A., Brandsch, R. & von Kiedrowski, G. Surface-promoted replication and exponential amplification of DNA analogues. Nature 396, 245–248 (1998).

    Article  CAS  Google Scholar 

  24. Röthlingshöfer, M. & Richert, C. Chemical primer extension at submillimolar concentration of deoxynucleotides. J. Org. Chem. 75, 3945–3952 (2010).

    Article  Google Scholar 

  25. Lohrmann, R., Bridson, P. K. & Orgel, L. E. Efficient metal-ion catalyzed template-directed oligonucleotide synthesis. Science 208, 1464–1465 (1980).

    Article  CAS  Google Scholar 

  26. Inoue, T. & Orgel, L. E. Substituent control of the poly (C)-directed oligomerization of guanosine 5′-phosphoroimidazolide. J. Am. Chem. Soc. 103, 7667–7669 (1981).

    Article  Google Scholar 

  27. Lorsch, J. R., Bartel, D. P. & Szostak, J. W. Reverse transcriptase reads through a 2′–5′ linkage and a 2′-thiophosphate in a template. Nucleic Acids Res. 23, 2811–2814 (1995).

    Article  CAS  Google Scholar 

  28. Bartel, D. P. in The RNA World 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 143–161 (Cold Spring Harbor Laboratory Press, 1999).

  29. Powner, M. W., Gerland, B. & Sutherland, J. D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239–242 (2009).

    Article  CAS  Google Scholar 

  30. Reader J. S. & Joyce, G. F. A ribozyme composed of only two different nucleotides. Nature 420, 841–844 (2002).

    Article  CAS  Google Scholar 

  31. Sarracino, D. & Richert, C. Quantitative MALDI-TOF spectrometry of oligonucleotides and a nuclease assay. Bioorg. Med. Chem. Lett. 6, 2543–2548 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank J. Fanous for measuring hydrolysis rates, and E. Kervio, H. Vogel, S. Vogel and U. Steiner for discussions. A grant from DFG (no. RI 1063/8-1 to C.R.) and EU COST action CM0703 supported this research.

Author information

Authors and Affiliations

  1. Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart, 70569, Germany

    Christopher Deck, Mario Jauker & Clemens Richert

Authors
  1. Christopher Deck
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mario Jauker
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Clemens Richert
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.R. conceived the project and wrote the manuscript. C.D. designed the experiments, analysed the data and co-wrote the manuscript.

Corresponding author

Correspondence to Clemens Richert.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 657 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Deck, C., Jauker, M. & Richert, C. Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nature Chem 3, 603–608 (2011). https://doi.org/10.1038/nchem.1086

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.1086

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing