SELECTIVELY C-13-ENRICHED DNA - DYNAMICS OF THE C1'-H1' VECTOR IN D(CGCAAATTTGCG)(2)

In order to examine the internal dynamic processes of the dodecamer d( CGCAAATTTGCG)(2), the C-13- enriched oligonucleotide has been synthesi zed. The three central thymines were selectively C-13-labeled at the C 1' position and their spin-lattice relaxation parameters R(C-Z), R(C-X ,C-Y), R(H-Z-->C-Z), R(HZCZ), R(2H(Z)C(X,Y)) and R(H-Z(C)) were measur ed. Density functions were computed for two models of internal motions . Comparisons of the experimental data were made with the spin-lattice relaxation rates rather than with the density functions, whose values were altered by accumulation of the uncertainties of each relaxation rate measurement. The spin-lattice relaxation rates were computed with respect to the motions of the sugar around the C1'-N1 bond. A two-sta te jump model between the anti- and syn-conformations with P(anti)/P(s yn) = 91/9 or a restricted rotation model with Delta(chi) = 28 degrees and an internal diffusion coefficient of 30 x 10(7) s(-1) gave a good fit with the experimental data. Twist, tilt or roll base motions have little effect on (13)C1' NMR relaxation. Simulation of spin-relaxatio n rates with the data obtained at several temperatures between 7 and 3 2 degrees C, where the dodecamer is double stranded, shows that the in ternal motion amplitude is independent of the temperature within this range, as expected for internal motion. Using the strong correlation w hich exists in a B-DNA structure between the chi and delta angle, we s uggest that the change in the glycosidic angle value should be indicat ive of a sugar puckering between the C1'-exo and CT-endo conformations .