A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies

Two crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x-ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623-635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x-ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669-6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5' end) and dGn stretches (at the 3' end) of different lengths, on the conformational flexibility of the nucleic acid, is considered.