Spectral assignment of the base protons, H-l',H-2', and H-2'', of both the dAp and pdA portions of dApdA has been made. The results indicate that dApdA has an anti,anti right-handed conformation with extensive base-base interaction. Four coupling constants, J1'_2'' (cis), J1'-2' (trans), J2'_3' (cis), and J2'-3' (trans), of the furanose of both the dAp and pdA portions of dApdA, 3 '-dAMP, and 5'-dAMP were determined by first-order analysis of 220-MHz spectra and 100-MHz spectra. The data show that the coupling constants between the dAp and pdA portions of dApdA are similar to those of 3'-dAMP and 5'-dAMP, while the coupling constants of 3'-dAMP and 5'-dAMP are not the same. Through the application of the Karplus equation, four dihedral angles, ɸ1'_2'' (cis), ɸ1'_2' (trans), ɸ2'-3' (cis), and ɸ2'_3'' (trans), were determined. These analyses suggest that the furanose conformation for 3'-dAMP and dAp in dApdA is that of C(2')-endo (envelope) or C(2')-endo-C(3')-exo (twisted form), while the furanose conformation for 5'-dAMP and pdA in dApdA is that of a rapid equilibrium between C(2')-endo and C(3')-endo. From the temperature and solvent studies of the J1'-2' values of 5'-dAMP and dApdA, it is suggested that the formation of intermolecular stacks of 5'-dAMP or the formation of intra-nucleotidyl stacking of dApdA does not cause a change in the furanose conformation.
ASJC Scopus subject areas
- Colloid and Surface Chemistry