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Nucleic Acids Research, 1983, Vol. 11, No. 13 4583-4600
© 1983

CHEMISTRY

Conformational analysis of oligoarabinonucleotides. An NMR and CD study*

Johannes Doornbos, Jean-Louis Barascut1, Hassan Lazrek1, Jean-Louis Imbach1, Jeroen van Westrenen, Gerben M. Visser, Jacques H. van Boom and Cornelis Altona

1Université des Sciences et Techniques du Languedoc Place Eugène Bataillon, 34060 Montpellier, France Gorlaeus Laboratories, Department of Chemistry, State University Leiden P.O.Box 9502, NL-2300 RA Leiden, The Netherlands

Received April 12, 1983. Revised June 8, 1983. Accepted June 8, 1983.

A 500 and 300 MHz proton NMR study of the series of oligoarabinonucleotides 5'aAMP, 3'aAMP, aA-aA, (aA-)2aA and (aA-)3-aA is presented. In addition, circular dichroism is used to study the stacking behaviour of aA-aA. The complete 1H-NMR spectral assignment of the compounds (except the tetramer) is given. Proton-proton and proton-phosphorus coupling constants, obtained by computer simulation of the high-field region of the spectra, yield information on the conformation of the arabinose rings (N- or S-type) and on the intramolecular stacking properties of the dimer and the trimer. The monomers 5'aAMP and 3'aAMP exhibit a preference for N- and S-type sugar conformation, respectively. It is shown that the dimer aA-aA at low temperature prefers a mixed stacked state of the type aA(S)-aA(N). In the trimer the aA(2)-aA(3) fragment exhibits a conformation similar to that found in the dimer, whereas the aA(l) residue prefers to adopt S-type sugar and has some tendency to stack upon residue aA(2).

*This paper is no.32 in the series ‘Nucleic Acids Constituents’. For no.31 see previous paper


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