Selectively13C-Enriched DNA: Dynamics of the C1′H1′ and C5′H5′ or C5′H5″ Vectors in d(CGCAAATTTGCG)2

Abstract

In order to examine the internal dynamic processes of the dodecamer d(CGCAAATTTGCG)2, the 13C-enriched oligonucleotide was synthesized. The C3, A4 and A6 residues were selectively 13C labeled at the C1′ and C5′ positions and their R(Cx,y), R(Cz) and R(Hz→Cz) 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 τg, S2 and τi. 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 τg value of 3.7 ns at 32°C, in agreement with those computed from independent 13C 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 (τex=130 μs) which can reflect special dynamics of the tract AAATTT which supports the spine of hydration. Analysis of 13C relaxation rates indicated smaller order parameters S2 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. © 1997 by John Wiley & Sons, Ltd.