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.

Structural genomics of RNA

Abstract

A detailed understanding of the functions and interactions of biological macromolecules requires knowledge of their molecular structures. Structural genomics, the systematic determination of all macromolecular structures represented in a genome, is focused at present exclusively on proteins. It is clear, however, that RNA molecules play a variety of significant roles in cells, including protein synthesis and targeting, many forms of RNA processing and splicing, RNA editing and modification, and chromosome end maintenance. To comprehensively understand the biology of a cell, it will ultimately be necessary to know the identity of all encoded RNAs, the molecules with which they interact and the molecular structures of these complexes. This report focuses on the feasibility of structural genomics of RNA, approaches to determining RNA structures and the potential usefulness of an RNA structural database for both predicting folds and deciphering biological functions of RNA molecules.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Secondary structure of the group I class of self-splicing introns.
Figure 2: Solution and crystal structures of the 50-nucleotide domain IV of signal recognition particle 4.5S RNA.

References

  1. Mitchell, J.R., Cheng, J. & Collins, K. Mol. Cell. Biol. 19, 567– 576 (1999).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Moore, P.B. Annu. Rev. Biochem. 68, 287–300 (1999).

    CAS  Article  PubMed  Google Scholar 

  3. Leontis, N.B. & Westhof, E. Quart. Rev. Biophys. 31, 399–455 (1998).

    CAS  Article  Google Scholar 

  4. Schmitz, U. et al. RNA 5, 1419–1429 (1999).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Batey, R.T., Rambo, R.P., Lucast, L., Rha, B. & Doudna, J.A. Science 287, 1232– 1239 (2000).

    CAS  Article  PubMed  Google Scholar 

  6. Jovine, L. et al. Structure 8, 527–540 (2000).

    CAS  Article  PubMed  Google Scholar 

  7. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. Science 289, 905– 920 (2000).

    CAS  Article  PubMed  Google Scholar 

  8. Ferre-D'Amare, A.R., Zhou, K. & Doudna, J.A. Nature 395, 567– 574 (1998).

    CAS  Article  PubMed  Google Scholar 

  9. Cate, J.H. et al. Science 273, 1678–1685 (1996).

    CAS  Article  PubMed  Google Scholar 

  10. Butcher, S.E., Dieckmann, T. & Feigon, J. EMBO J. 16, 7490– 7299 (1997).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Bourdeau, V., Ferbeyre, G., Pageau, M., Paquin, B. & Cedergren R. Nucleic Acids. Res. 27, 4457– 4467 (1999).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  12. Lowe, T.M. & Eddy, S.R. Science 283, 1168–1171 (1999).

    CAS  Article  PubMed  Google Scholar 

  13. Omer, A.D. et al. Science 288, 517–522 (2000).

    CAS  Article  PubMed  Google Scholar 

  14. Latham, J.A. & Cech, T.R. Science 245, 276–282 (1989).

    CAS  Article  PubMed  Google Scholar 

  15. Christian, E.L. & Yarus, M. J. Mol. Biol. 228, 743–758 (1992).

    CAS  Article  PubMed  Google Scholar 

  16. Harris, M.E., Kazantsev, A.V., Chen, J.L. & Pace, N.R. RNA 3, 561–576 ( 1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Ryder, S.P., Ortoleva-Donnelly, L., Kosek, A.B. & Strobel, S.A. Methods Enzymol. 317, 92–109 (2000).

    CAS  Article  PubMed  Google Scholar 

  18. Stowell, M.H., Miyazawa, A. & Unwin, N. Curr. Opin. Struct. Biol. 8, 595–600 (1998).

    CAS  Article  PubMed  Google Scholar 

  19. Ferre-D'Amare, A.R. & Doudna, J.A. Nucleic Acids Res. 24, 977–978 ( 1996).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Doudna, J.A., Grosshans, C., Gooding, A. & Kundrot, C.E. Proc. Natl. Acad. Sci. USA 90, 7829– 7833 (1993).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Scott, W.G. et al. J. Mol. Biol. 250, 327– 332 (1995).

    CAS  Article  PubMed  Google Scholar 

  22. Golden, B.L., Podell, E.R., Gooding, A.R. & Cech, T.R. J. Mol. Biol. 270, 711–723 (1997).

    CAS  Article  PubMed  Google Scholar 

  23. Ferre-D'Amare, A.R., Zhou, K., Doudna, J.A. J. Mol. Biol. 279, 621–631 (1998).

    CAS  Article  PubMed  Google Scholar 

  24. Ferre-D'Amare, A.R. & Doudna, J.A. J. Mol. Biol. 295, 541–556 ( 2000).

    CAS  Article  PubMed  Google Scholar 

  25. Burley, S.K. et al. Nature Genet. 23, 151– 157 (1999).

    CAS  Article  PubMed  Google Scholar 

  26. Michel, F. & Westhof, E. J. Mol. Biol. 216, 585–610 (1990).

    CAS  Article  PubMed  Google Scholar 

  27. Golden, B.L., Gooding, A.R., Podell, E.R. & Cech, T.R. Science 282, 259–264 ( 1998).

    CAS  Article  PubMed  Google Scholar 

  28. Tanner, N.K. et al. Curr. Biol. 4, 488– 498 (1994).

    CAS  Article  PubMed  Google Scholar 

  29. Schluenzen, F. et al. Cell 102, 615 ( 2000).

    CAS  Article  PubMed  Google Scholar 

  30. Wimberly, B.T. et al. Nature 407, 327–339 (2000).

    CAS  Article  PubMed  Google Scholar 

  31. Carter, A.P. et al. Nature 407, 340–348 (2000).

    CAS  Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Doudna, J. Structural genomics of RNA. Nat Struct Mol Biol 7, 954–956 (2000). https://doi.org/10.1038/80729

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/80729

Further reading

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