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.

A tetrameric DNA structure with protonated cytosine-cytosine base pairs

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1

    Marsh, R. E., Bierstedt, R. & Eichhorn, E. L. Acta. crystallogr. 15, 310–316 (1962).

    CAS  Article  Google Scholar 

  2. 2

    Akrinimiski, E. O., Sander, C. & Ts'o, P. O. P. Biochemistry 2, 340–344 (1963).

    Article  Google Scholar 

  3. 3

    Hartman, K. A. Jr & Rich, A. J. Am. Chem. Soc. 87, 2033–2039 (1965).

    CAS  Article  Google Scholar 

  4. 4

    Inman, R. B. J. molec. Biol. 9, 624–637 (1964).

    CAS  Article  Google Scholar 

  5. 5

    Langridge, R. & Rich, A. Nature 198, 725–728 (1963).

    ADS  CAS  Article  Google Scholar 

  6. 6

    Arnott, S., Chandrasekaran, R. & Leslie, A. G. W. J. molec. Biol. 106, 735–748 (1976).

    CAS  Article  Google Scholar 

  7. 7

    Westhof, E., Roa, S. T. & Sundaralingam, M. J. molec. Biol. 142, 331–361 (1980).

    CAS  Article  Google Scholar 

  8. 8

    Westhof, E. & Sundaralingam, M. Proc. natn. Acad. Sci. U.S.A. 77, 1852–1856 (1980).

    ADS  CAS  Article  Google Scholar 

  9. 9

    Luo, J., Sarma, M. H., Yuan, R. & Sarma, R. H. FEBS Lett. 306, 223–228 (1992).

    CAS  Article  Google Scholar 

  10. 10

    Leroy, J.-L., Kettani, A., Kochoyan, M. & Guéron, M. Abstr. XIV Int. Conf. Magn. Reson. in Biol. Systems, Warwick (1990).

  11. 11

    Leroy, J.-L., Gehring, K. & Gueron, M. Abstr. XV Int. Conf. Magn. Reson. In Biol. Systems, Jerusalem (1992).

  12. 12

    Leroy, J.-L. et al. Biochemistry (in the press).

  13. 13

    Aboul-ela, F., Murchie, A. I. H. & Lilley, D. M. J. Nature 360, 280–282 (1992).

    ADS  CAS  Article  Google Scholar 

  14. 14

    Kellogg, G. W. J. magn. Reson. 98, 176–182 (1992).

    ADS  CAS  Google Scholar 

  15. 15

    Brünger, A. T. X-PLOR (Version 2.1) Manual (Yale Univ., Connecticut, 1990).

    Google Scholar 

  16. 16

    EMBO Workshop, EMBO J. 8, 1–4 (1989).

  17. 17

    Altona, C. Recl. Chim. Pays Bas 101, 413–433 (1982).

    CAS  Article  Google Scholar 

  18. 18

    Kistenmacher, T. J., Rossi, M. & Marzilli, L. G. Biopolymers 17, 2581–2585 (1978).

    CAS  Article  Google Scholar 

  19. 19

    Lyamichev, V. I. et al. Nature 339, 634–637 (1989).

    ADS  CAS  Article  Google Scholar 

  20. 20

    Ahmed, S. & Henderson, E. Nucleic Acids Res. 20, 507–511 (1992).

    CAS  Article  Google Scholar 

  21. 21

    Blackburn, E. H. Nature 350, 569–572 (1991).

    ADS  CAS  Article  Google Scholar 

  22. 22

    Sen, D. & Gilbert, W. Nature 334, 364–366 (1988).

    ADS  CAS  Article  Google Scholar 

  23. 23

    Sundquist, W. I. & Klug, A. Nature 342, 825–829 (1989).

    ADS  CAS  Article  Google Scholar 

  24. 24

    Smith, F. W. & Feigon, J. Nature 356, 164–168 (1992).

    ADS  CAS  Article  Google Scholar 

  25. 25

    Kang, C., Zhang, X., Ratliff, R., Moyzis, R. & Rich, A. Nature 356, 126–131 (1992).

    ADS  CAS  Article  Google Scholar 

  26. 26

    Kochoyan, M., Leroy, J.-L. & Guéron, M. Biochemistry 29, 4799–4805 (1990).

    CAS  Article  Google Scholar 

  27. 27

    Westhof, E. Nature 358, 459 (1992).

    ADS  CAS  Article  Google Scholar 

  28. 28

    Wüthrich, K. NMR of Proteins and Nucleic Acids 211 (Wiley, New York, 1986).

    Google Scholar 

Download references

Author information

Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

Further reading

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.

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