Selectively C-13-enriched DNA: Dynamics of the C1'H1' and C5'H5' or C5'H5'' vectors in d(CGCAAATTTGCG)(2)

In order to examine the internal dynamic processes of the dodecamer d(CGCAAATTTGCG)(2),the C-13-enriched oligonucleotide was synthesized. The C3, A4 and A6 residues were selectively C-13 labeled at the C1' and C5' positions and their R(C-x,C-y), R(C-z) and R(H-z-->C-z) relaxation rates were measured. Data variations were observed for the three residues. The analysis of the relaxation rates in the context of the model-free formalism of Lipari and Szabo indicates other pathways than those described by tau(g), S-2 and tau(l). Direct evidence for the presence of a conformational exchange process was obtained for the residue A4 from rotating frame relaxation measurements. Taking into account the exchange process contribution, analysis of these data gave a tau(g) value of 3.7 ns at 32 degrees C, in agreement with those computed from independent C-13 relaxation rate measurements on the three thymines or from the H5-H6 NOE measurements. The frequency difference between the exchanging sites was computed in the range 130-250 Hz. This additional relaxation process involves large amplitude and slow motions (tau(ex) = 130 mu s) which can reflect special dynamics of the tract AAATTT which supports the spine of hydration. Analysis of C-13 relaxation rates indicated smaller order parameters S-2 for C5' (0.40) than for C1' (0.80). These data reflected additional motions undergone by the C5'H5' or C5 '' H5 '' vectors such as repuckering and motions around the C4'-C5' bond. (C) 1997 by John Wiley & Sons, Ltd.