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.

  • Commentary
  • Published:

Using synthetic RNAs as scaffolds and regulators

Abstract

The natural versatility of RNA makes it an ideal substrate for bioengineering. Its structural properties and predictable base-pairing permit its use as molecular scaffold, and its ability to interact with nucleic acids, proteins and small molecules confers a regulatory potential that can be harvested to design RNA regulators in diverse contexts.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

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

Figure 1: RNA structures produced to date and examples of reactions that they have been used to catalyze.
Figure 2: Mechanisms and applications of synthetic-RNA regulation.

References

  1. Zappulla, D.C. & Cech, T.R. Proc. Natl. Acad. Sci. USA 101, 10024–10029 (2004).

    Article  CAS  Google Scholar 

  2. Tsai, M.-C. et al. Science 329, 689–693 (2010).

    Article  CAS  Google Scholar 

  3. SantaLucia, J. Proc. Natl. Acad. Sci. USA 95, 1460–1465 (1998).

    Article  CAS  Google Scholar 

  4. Chworos, A. et al. Science 306, 2068–2072 (2004).

    Article  CAS  Google Scholar 

  5. Severcan, I. et al. Nat. Chem. 2, 772–779 (2010).

    Article  CAS  Google Scholar 

  6. Geary, C., Rothemund, P.W.K. & Andersen, E.S. Science 345, 799–804 (2014).

    Article  CAS  Google Scholar 

  7. Delebecque, C.J., Lindner, A.B. & Silver, P. Science 333, 470–474 (2011).

    Article  CAS  Google Scholar 

  8. Myhrvold, C., Dai, M. & Silver, P. Nano Lett. 13, 4242–4248 (2013).

    Article  CAS  Google Scholar 

  9. Castellana, M. et al. Nat. Biotechnol. 32, 1011–1018 (2014).

    Article  CAS  Google Scholar 

  10. Fu, J., Liu, M., Liu, Y., Woodbury, N.W. & Yan, H. J. Am. Chem. Soc. 134, 5516–5519 (2012).

    Article  CAS  Google Scholar 

  11. Sachdeva, G., Garg, A., Godding, D., Way, J.C. & Silver, P.A. Nucleic Acids Res. 42, 9493–9503 (2014).

    Article  CAS  Google Scholar 

  12. Chen, X. & Ellington, A.D. PLOS Comput. Biol. 5, e1000620 (2009).

    Article  Google Scholar 

  13. Chen, Y.-J. et al. Nat. Methods 10, 659–664 (2013).

    Article  CAS  Google Scholar 

  14. Na, D. et al. Nat. Biotechnol. 31, 170–174 (2013).

    Article  CAS  Google Scholar 

  15. Takahashi, M.K. & Lucks, J.B. Nucleic Acids Res. 41, 7577–7588 (2013).

    Article  CAS  Google Scholar 

  16. Green, A.A., Silver, P.A., Collins, J.J. & Yin, P. Cell 159, 925–939 (2014).

    Article  CAS  Google Scholar 

  17. Gilbert, L.A. et al. Cell 154, 442–451 (2013).

    Article  CAS  Google Scholar 

  18. Chen, Y.Y., Jensen, M.C. & Smolke, C.D. Proc. Natl. Acad. Sci. USA 107, 8531–8536 (2010).

    Article  CAS  Google Scholar 

  19. Pardee, K. et al. Cell 159, 940–954 (2014).

    Article  CAS  Google Scholar 

  20. Takahashi, M.K. et al. ACS Synth. Biol. doi:10.1021/sb400206c (28 March 2014).

  21. Zadeh, J.N. et al. J. Comput. Chem. 32, 170–173 (2011).

    Article  CAS  Google Scholar 

  22. Kosuri, S. et al. Nat. Biotechnol. 28, 1295–1299 (2010).

    Article  CAS  Google Scholar 

  23. Ravikumar, A., Arrieta, A. & Liu, C.C. Nat. Chem. Biol. 10, 175–177 (2014).

    Article  CAS  Google Scholar 

  24. Whitaker, W.R. & Davis, S. Proc. Natl. Acad. Sci. USA 109, 18090–18095 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank L. Liu, S. Hays and R. Chang for feedback while writing this commentary. Some of the work described here was funded by Defense Advanced Research Projects Agency award HR0011-12-C-0061 to P.A.S. C.M. is funded by the Fannie and John Hertz Foundation.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Cameron Myhrvold or Pamela A Silver.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Myhrvold, C., Silver, P. Using synthetic RNAs as scaffolds and regulators. Nat Struct Mol Biol 22, 8–10 (2015). https://doi.org/10.1038/nsmb.2944

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2944

This article is cited by

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