Using synthetic RNAs as scaffolds and regulators

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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.

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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. 1

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

  2. 2

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

  3. 3

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

  4. 4

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

  5. 5

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

  6. 6

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

  7. 7

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

  8. 8

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

  9. 9

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

  10. 10

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

  11. 11

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

  12. 12

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

  13. 13

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

  14. 14

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

  15. 15

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

  16. 16

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

  17. 17

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

  18. 18

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

  19. 19

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

  20. 20

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

  21. 21

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

  22. 22

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

  23. 23

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

  24. 24

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

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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.

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Correspondence to Cameron Myhrvold or Pamela A Silver.

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The authors declare no competing financial interests.

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

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