Abstract
OLIGOMERS containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5′-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and con-strained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs HI′-HI′, Hl′-H2" and H1′-H4′. These NOEs are probably diagnostic for such tetrameric structures.
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Marsh, R. E., Bierstedt, R. & Eichhorn, E. L. Acta. crystallogr. 15, 310–316 (1962).
Akrinimiski, E. O., Sander, C. & Ts'o, P. O. P. Biochemistry 2, 340–344 (1963).
Hartman, K. A. Jr & Rich, A. J. Am. Chem. Soc. 87, 2033–2039 (1965).
Inman, R. B. J. molec. Biol. 9, 624–637 (1964).
Langridge, R. & Rich, A. Nature 198, 725–728 (1963).
Arnott, S., Chandrasekaran, R. & Leslie, A. G. W. J. molec. Biol. 106, 735–748 (1976).
Westhof, E., Roa, S. T. & Sundaralingam, M. J. molec. Biol. 142, 331–361 (1980).
Westhof, E. & Sundaralingam, M. Proc. natn. Acad. Sci. U.S.A. 77, 1852–1856 (1980).
Luo, J., Sarma, M. H., Yuan, R. & Sarma, R. H. FEBS Lett. 306, 223–228 (1992).
Leroy, J.-L., Kettani, A., Kochoyan, M. & Guéron, M. Abstr. XIV Int. Conf. Magn. Reson. in Biol. Systems, Warwick (1990).
Leroy, J.-L., Gehring, K. & Gueron, M. Abstr. XV Int. Conf. Magn. Reson. In Biol. Systems, Jerusalem (1992).
Leroy, J.-L. et al. Biochemistry (in the press).
Aboul-ela, F., Murchie, A. I. H. & Lilley, D. M. J. Nature 360, 280–282 (1992).
Kellogg, G. W. J. magn. Reson. 98, 176–182 (1992).
Brünger, A. T. X-PLOR (Version 2.1) Manual (Yale Univ., Connecticut, 1990).
EMBO Workshop, EMBO J. 8, 1–4 (1989).
Altona, C. Recl. Chim. Pays Bas 101, 413–433 (1982).
Kistenmacher, T. J., Rossi, M. & Marzilli, L. G. Biopolymers 17, 2581–2585 (1978).
Lyamichev, V. I. et al. Nature 339, 634–637 (1989).
Ahmed, S. & Henderson, E. Nucleic Acids Res. 20, 507–511 (1992).
Blackburn, E. H. Nature 350, 569–572 (1991).
Sen, D. & Gilbert, W. Nature 334, 364–366 (1988).
Sundquist, W. I. & Klug, A. Nature 342, 825–829 (1989).
Smith, F. W. & Feigon, J. Nature 356, 164–168 (1992).
Kang, C., Zhang, X., Ratliff, R., Moyzis, R. & Rich, A. Nature 356, 126–131 (1992).
Kochoyan, M., Leroy, J.-L. & Guéron, M. Biochemistry 29, 4799–4805 (1990).
Westhof, E. Nature 358, 459 (1992).
Wüthrich, K. NMR of Proteins and Nucleic Acids 211 (Wiley, New York, 1986).
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Gehring, K., Leroy, JL. & Guéron, M. A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature 363, 561–565 (1993). https://doi.org/10.1038/363561a0
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DOI: https://doi.org/10.1038/363561a0
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