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Nucleic Acids Research, 1984, Vol. 12, No. 10 4323-4338
© 1984

CHEMISTRY

Conformational analysis of r(CGCGCG) in aqueous solution: an A-type double helical conformation studied by two-dimensional nuclear Overhauser effect spectroscopy

H.P. Westerink, G.A. van der Marel, J.H. van Boom and C.A.G. Haasnoot+,*

Gorlaeus Laboratories, State University P.O. Box 9502, 2300 RA Leiden, The Netherlands +Department of Biophysical Chemistry, Faculty of Science, University of Nijmegen Toernooiveld, 6525 ED Nijmegen, The Netherlands

*To whom correspondence should be addressed

Received March 2, 1984. Revised April 27, 1984. Accepted April 27, 1984.

The conformation of the hexanucleoside pentaphosphate r(CGCGCG) in aqueous solution was studied by circular dichroism, 1H- and 31P-NMR spectroscopy. The base-, H1'- and H2'-proton resonances were assigned by means of 2D-NOE spectroscopy. The base- and H1'-proton chemical shifts were studied as a function of temperature. Proton-proton distances are computed in A- and A'-RNA as well as in A-, B- and Z-DNA. A qualitative interpretation of the observed 2D-NOE intensities shows that r(CGCGCG) adopts a regular A-type double helical conformation under our experimental conditions. The CD- and 31P-NMR experiments described in this paper are in agreement with this structure both under low-and high-salt conditions.


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