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

Abstract

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.

Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy

“…In this interval, the band appearing near 1373 cm −1 in our study denotes contributions from the dA and dG residues (C2 -endo/anti). Similar results were also reported by several authors [32,39,41]. Another strong peak appeared near 1419 cm −1 and is attributed to the C2 -endo/anti sugar pucker (B-form) [32,39].…”

“…Similar results were also reported by several authors [32,39,41]. Another strong peak appeared near 1419 cm −1 and is attributed to the C2 -endo/anti sugar pucker (B-form) [32,39]. Furthermore, in the region of 1500 cm −1 -1800 cm −1 , vibrations sensitive to base pairing and base stacking interactions appeared as previously reported by Lindqvist and Gräslund (2001) [53].…”

“…An UPGMA [61] (pp. [39][40][41][42] dendrogram was also constructed based on a symmetric dissimilarity matrix using the SHAN module in NTSYS program, version 2.1 [62]. The COPH and MXCOMP modules of NTSYS 2.1 were used to check the goodness-of-fit between the cluster analysis and dissimilarity matrix.…”

The Influence of UV Femtosecond Laser Pulses on Bacterial DNA Structure, as Proved by Fourier Transform Infrared (FT‐IR) Spectroscopy

“…A low intensity band is found at 782 cm −1 for DNA from E. coli B, around 780 cm −1 for E. coli C nucleic acids and near 778 cm −1 for the DNA isolated from Salmonella E, being attributed to deoxy C3′‐ endo −O−P−O (possible A‐form) [15] …”

“…[9] A low intensity band is found at 782 cm À 1 for DNA from E. coli B, around 780 cm À 1 for E. coli C nucleic acids and near 778 cm À 1 for the DNA isolated from Salmonella E, being attributed to deoxy C3'-endoÀ OÀ PÀ O (possible A-form). [15] A very weak FT-IR band can be observed around 833 cm À 1 in the DNA spectra corresponding to E. coli A and E. coli C strains, being shifted to 850 cm À 1 in the case of E. coli B nucleic acid spectrum. This weak spectral contribution is not visible in any of the nucleic acids from E. coli D and Salmonella strains Figure 2.…”