Abstract
HAIRPIN loops are important structural elements of RNA, helping to define the three-dimensional structure of large RNAs and providing potential nucleation sites for RNA folding and interaction with other nucleic acids and proteins1–3. Little, however, is known about the conformation of RNA hairpins, most of what we know coming from transfer RNA crystal structures4 and from studies of DNA hairpins5–8. We report here the determination of the structure of a very stable and common RNA hairpin, 5'GGAC(UUCG)G(JCC (loop nucleotides in parenthesis), by NMR spectroscopy. The sequence C(UUCG)G occurs very often in RNA9 and may be a nucleation site for RNA folding and a protein-binding site. A high-resolution structure for the hairpin was derived from interproton distances and scalar coupling constants determined by NMR. The loop is stabilized by a G o U base pair, with guanine in the syn conformation, a cytosine–phosphate contact and extensive base stacking. These findings and other structural features of the loop can explain the unusual stability of the hairpin and suggest why reverse transcriptase cannot read through the loop9, although it can transcribe through other kinds of RNA secondary structure.
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References
Carey, J., Cameron, V., de Haseth, P. L. & Uhlenbeck, O. C. Biochemistry 22, 2601–2610 (1983).
Feng, S. & Holland, E. C. Nature 334, 165–167 (1988).
Witherell, G. W. & Uhlenbeck, O. C. Biochemistry 28, 71–76 (1989).
Kim, S.-H. et al. Science 179, 285–288 (1973).
Chattopadhayaya, R., Ikuta, S., Greskowiak, K. & Dickerson, R. E. Nature 334, 175–179 (1988).
Hare, D. R. & Reid, B. R. Biochemistry 25, 5341–5350 (1986).
Blommers, M. J. J. et al. Biochemistry 28, 7491–7498 (1989).
Williamson, J. R. & Boxer, S. G. Biochemistry 28, 2819–2831 (1989).
Tuerk, C. et al. Proc. natn. Acad. Sci. U.S.A. 85, 1364–1368 (1988).
Cheong, C. thesis, Univ. California, Berkeley (1989).
Groebe, D. R. & Uhlenbeck, O. C. Nucleic Acids Res. 16, 11725–11735 (1988).
Wüthrich, K. NMR of Proteins and Nucleic Acids (Wiley, New York, 1986).
Varani, G., Wimberly, B. & Tinoco, I., Jr Biochemistry 28, 7760–7772 (1989).
Altona, C. Recl Trav. chim. Pays-Bas Belg. 101, 413–433 (1982).
Lankhorst, P. P., Haasnoot, C. A. G., Erkelens, C. & Altona, C. J. Biomol. Struct. Dyn. 1, 1387–1405 (1984).
Gorenstein, D. in 31P NMR, Principles and Applications (Academic, New York, 1984).
Kollman, P., Weiner, P. & Dearing, A. Biopolymers 20, 2583–2611 (1981).
Moazed, D., Stern, S. & Noller, H. F. J. molec. Biol. 187, 399–416 (1986).
Saenger, W. Principles of Nucleic Acid Structure (Springer-Verlag, New York, 1984).
Milligan, J. F., Groebe, D. R., Witherell, G. W. & Uhlenbeck, O. C. Nucleic Acids Res. 15, 8783–8798 (1987).
Sklenar, V, Miyoshiro, H., Zon, G. & Bax, A. FEBS Lett. 208, 94–98 (1986).
Frey, M. H. et al. Biopolymers 24, 2371–2380 (1985).
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Cheong, C., Varani, G. & Tinoco, I. Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC. Nature 346, 680–682 (1990). https://doi.org/10.1038/346680a0
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DOI: https://doi.org/10.1038/346680a0
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