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

Abstract

Abstract Two crystals d(C 2 GCG 2 ) and d(C 5 GCG 5 ) 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(C 5 GCG 5 ) 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(C 2 GCG 2 ) 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 dC n stretches (at the 5′ end) and dG n stretches (at the 3′ end) of different lengths, on the conformational flexibility of the nucleic acid, is considered. © 1993 John Wiley & Sons, Inc.