RNA bulges and the helical periodicity of double-stranded RNA

Abstract

RNA MOLECULES typically exhibit extensive secondary structure, including double-stranded duplex, hairpins, internal loops, bulged bases and pseudoknotted1,2 structures (reviewed in refs 3 and 4). This is intimately connected with biological function, including splicing reactions5,6 and ribozyme activity7,8. The formation of RNA–DNA hybrids is important in the transcription of DNA, reverse transcription of viral RNA, and DNA replication. Bulged bases in RNA helices are potentially significant in RNA folding and in providing sites for specific protein–RNA interactions, as illustrated by TFIIIA of Xenopus9and the coat protein of phage R17 (ref. 10). Most information about the structure of RNA derives from fibre diffraction11,12 or crystallography of natural molecules, notably transfer RNA13–17, but until recently there have been few systematic studies of RNA structure using designed sequences18–22. We have used gel electrophoresis to investigate the properties of bulged bases in both RNA and RNA–DNA duplexes in solution. As in DNA helices23–25, bulges introduce pronounced kinks into RNA and into RNA–DNA helices, depending on the number and types of bases in the bulge and its position in the fragment. By varying the spacing between two bulge-induced kinks, we have measured the periodicity of RNA and RNA–DNA helices in solution.

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References

  1. 1

    Pleij, C. W. A., Rietveld, K. & Bosch, L. Nucleic Acids Res. 13, 1717–1731 (1985).

  2. 2

    Puglisi, J. D., Wyatt, J. R. & Tinoco Jr, I. Nature 321, 283–286 (1988).

  3. 3

    Delarue, M. & Moras, D. Nucleic Acids and Molecular Biology Vol. 3 (eds. Eckstein, F. & Lilley, D. M. J.), 182–196 (Springer-Verlag, Berlin and Heidelberg, 1989).

  4. 4

    Wyatt, J. R., Puglisi, J. D. & Tinoco Jr, I. BioEssays 11, 100–106 (1989).

  5. 5

    Cech, T. R. et al. Proc. natn. Acad. Sci. U.S.A. 80, 3903–3907 (1983).

  6. 6

    Inoue, T. & Cech, T. R. Proc. natn. Acad. Sci. U.S.A. 82, 648–652 (1985).

  7. 7

    Uhlenbeck, O. C. Nature 328, 596–600 (1987).

  8. 8

    Haseloff, J. & Gerlach, W. L. Nature 334, 585–591 (1988).

  9. 9

    Baudin, F. & Romaniuk, P. J. Nucleic Acids Res. 17, 2043–2056 (1989).

  10. 10

    Wu, H-N. & Uhlenbeck, O. C. Biochemistry 26, 8221–8227 (1987).

  11. 11

    Arnott, S., Fuller, W., Hodgson, A. & Prutton, I. Nature 220, 561–564 (1968).

  12. 12

    Arnott, S., Chandrasekharan, R., Millane, R. P. & Park, H.-S. J. molec. Biol. 188, 631–640 (1986).

  13. 13

    Quigley, G. J. et al. Proc. natn. Acad. Sci. U.S.A. 72, 4866–4870 (1975).

  14. 14

    Jack, A., Ladner, J. E. & Klug, A. J. molec. Biol. 108, 619–649 (1976).

  15. 15

    Moras, D. et al. Nature 288, 669–674 (1980).

  16. 16

    Shevitz, R. W. et al. Nature 278, 188–190 (1979).

  17. 17

    Woo, N. H., Roe, B. A. & Rich, A. Nature 286, 346–351 (1980).

  18. 18

    Wang, A. H-J. et al. Nature 299, 601–604 (1982).

  19. 19

    Dock-Bregeon, A. C. et al. Nature 335, 375–378 (1988).

  20. 20

    Varani, G., Wimberley, B. & Tinoco, I. Biochemistry 28, 7760–7772 (1989).

  21. 21

    Chou, S-H., Flynn, P. & Reid, B. Biochemistry 28, 2422–2435 (1989).

  22. 22

    Zhang, P. & Moore, P. B. Biochemistry 28, 4607–4615 (1989).

  23. 23

    Hsieh, C-H. & Griffith, J. D. Proc. natn. Acad. Sci. U.S.A. 86, 4833–4837 (1989).

  24. 24

    Bhattacharyya, A. & Lilley, D. M. J. Nucleic Acids Res. 17, 6821–6840 (1989).

  25. 25

    Rice, J. A. & Crothers, D. E. Biochemistry 28, 4512–4516 (1989).

  26. 26

    Woodson, S. A. & Crothers, D. M. Biochemistry 27, 3130–3141 (1988).

  27. 27

    Chou, S-H., Flynn, P. & Reid, B. Biochemistry 28, 2435–2443 (1989).

  28. 28

    Wu, H-M. & Crothers, D. E. Nature 308, 509–513 (1984).

  29. 29

    Rhodes, D. & Klug, A. Nature 292, 378–380 (1981).

  30. 30

    Peck, L. J. & Wang, J. C. Nature 292, 375–378 (1981).

  31. 31

    Beaucage, S. L. & Caruthers, M. H. Tetrahedron Lett. 22, 1859–1862 (1981).

  32. 32

    Sinha, N. D., Biernat, J., McManus, J. & Köster, H. Nucleic Acids Res. 12, 4539–4557 (1984).

  33. 33

    Milligan, J. F., Groebe, D. R., Witherell, G. & Uhlenbeck, O. C. Nucleic Acids Res. 21, 8783–8798 (1987).

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Bhattacharyya, A., Murchie, A. & Lilley, D. RNA bulges and the helical periodicity of double-stranded RNA. Nature 343, 484–487 (1990). https://doi.org/10.1038/343484a0

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