Determination of internal dynamics of deoxyriboses in the DNA hexamer d(CGTACG)2 by 1H NMR.

The conformations and internal dynamics of the deoxyriboses of d(CGTACG)2 have been determined by NMR measurements at 15 degrees C. The conformations of the sugars were determined using coupling constants and time-dependent NOE measurements. The J-splitting patterns of the H1', H2' and H2" resonances show that the sugars exist as mixtures of conformations near C2' endo (south) and C3' endo (north). The population of the south conformation was larger for the purines than for the pyrimidines. The overall tumbling time of the molecule in 2H2O was determined from measurements of the cross relaxation rate constant for the H6-H5 vectors of the two cytosine residues. Order parameters were determined for the H1'-H2", H2'-H2" and H2'-H3' vectors from measurements of cross relaxation rate constants, making use of multi-spin analysis of the NOE build up rates. These order parameters are weakly dependent of the base sequence, and except for the terminal Cyt 1 residue, the H2'-H2" and H2'-H3' vectors are near unity, indicating the absence of rapid pseudorotation on the nanosecond time scale. However, the order parameter for the H1'-H2" vector is significantly smaller than expected for rapid pseudorotation indicating the presence of other motions of the sugars. This motion must be about an effective axis parallel to the H2'-H2" vector, and to occur with an angular fluctuation of about 30 degrees. The results show that to obtain highly refined structures for nucleic acids by NMR the effects of spin diffusion and motional averaging cannot be ignored.