Solution conformations of d(CGTACG)₂ determined from NMR experiments

The conformations of all the nucleotides in the hexamer d(CGTACG)₂ have been determined using time-dependent one- and two-dimensional nuclear Overhauser enhancements (NOEs) and the program NUCFIT (see previous article). The glycosidic torsion angles are well determined, the fraction of the C2′ endo state for the sugar puckers is less well determined, and the pseudorotation phase angle is poorly determined by the NOEs. The average glycosidic torsion angle is -107 ± 9°, and the deoxyriboses of the purine residues have a higher fraction of the C2′ endo state than those of the pyrimidine residues. There is good agreement between the one- and two-dimensional NOE data. Of the helical parameters, the local rise and twist are moderately well determined, but the roll and tilt of the bases are not well described. The overall structure belongs to the B family of conformations, as previously described by Gronenborn et al. (Biochem. J. (1984) 221, 723-736), but there are significant differences which can be ascribed to the improved treatment of the spin-diffusion and motional averaging possible with the program NUCFIT. The results obtained using NUCFIT are compared with those from restrained energy minimisation calculations using distance restraints obtained from NUCFIT.