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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Pleij, C. W. A., Rietveld, K. & Bosch, L. Nucleic Acids Res. 13, 1717–1731 (1985).
Puglisi, J. D., Wyatt, J. R. & Tinoco Jr, I. Nature 321, 283–286 (1988).
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).
Wyatt, J. R., Puglisi, J. D. & Tinoco Jr, I. BioEssays 11, 100–106 (1989).
Cech, T. R. et al. Proc. natn. Acad. Sci. U.S.A. 80, 3903–3907 (1983).
Inoue, T. & Cech, T. R. Proc. natn. Acad. Sci. U.S.A. 82, 648–652 (1985).
Uhlenbeck, O. C. Nature 328, 596–600 (1987).
Haseloff, J. & Gerlach, W. L. Nature 334, 585–591 (1988).
Baudin, F. & Romaniuk, P. J. Nucleic Acids Res. 17, 2043–2056 (1989).
Wu, H-N. & Uhlenbeck, O. C. Biochemistry 26, 8221–8227 (1987).
Arnott, S., Fuller, W., Hodgson, A. & Prutton, I. Nature 220, 561–564 (1968).
Arnott, S., Chandrasekharan, R., Millane, R. P. & Park, H.-S. J. molec. Biol. 188, 631–640 (1986).
Quigley, G. J. et al. Proc. natn. Acad. Sci. U.S.A. 72, 4866–4870 (1975).
Jack, A., Ladner, J. E. & Klug, A. J. molec. Biol. 108, 619–649 (1976).
Moras, D. et al. Nature 288, 669–674 (1980).
Shevitz, R. W. et al. Nature 278, 188–190 (1979).
Woo, N. H., Roe, B. A. & Rich, A. Nature 286, 346–351 (1980).
Wang, A. H-J. et al. Nature 299, 601–604 (1982).
Dock-Bregeon, A. C. et al. Nature 335, 375–378 (1988).
Varani, G., Wimberley, B. & Tinoco, I. Biochemistry 28, 7760–7772 (1989).
Chou, S-H., Flynn, P. & Reid, B. Biochemistry 28, 2422–2435 (1989).
Zhang, P. & Moore, P. B. Biochemistry 28, 4607–4615 (1989).
Hsieh, C-H. & Griffith, J. D. Proc. natn. Acad. Sci. U.S.A. 86, 4833–4837 (1989).
Bhattacharyya, A. & Lilley, D. M. J. Nucleic Acids Res. 17, 6821–6840 (1989).
Rice, J. A. & Crothers, D. E. Biochemistry 28, 4512–4516 (1989).
Woodson, S. A. & Crothers, D. M. Biochemistry 27, 3130–3141 (1988).
Chou, S-H., Flynn, P. & Reid, B. Biochemistry 28, 2435–2443 (1989).
Wu, H-M. & Crothers, D. E. Nature 308, 509–513 (1984).
Rhodes, D. & Klug, A. Nature 292, 378–380 (1981).
Peck, L. J. & Wang, J. C. Nature 292, 375–378 (1981).
Beaucage, S. L. & Caruthers, M. H. Tetrahedron Lett. 22, 1859–1862 (1981).
Sinha, N. D., Biernat, J., McManus, J. & Köster, H. Nucleic Acids Res. 12, 4539–4557 (1984).
Milligan, J. F., Groebe, D. R., Witherell, G. & Uhlenbeck, O. C. Nucleic Acids Res. 21, 8783–8798 (1987).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/343484a0
This article is cited by
-
Three new mycoviruses identified in the apple replant disease (ARD)-associated fungus Rugonectria rugulosa
Virus Genes (2022)
-
3D maps of RNA interhelical junctions
Nature Protocols (2011)
-
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings
Nature Protocols (2007)
-
Ionic interactions and the global conformations of the hammerhead ribozyme
Nature Structural Biology (1995)
-
Determination of the DNA helical repeat by cryo-electron microscopy
Nature Structural & Molecular Biology (1994)
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.