Structure of the Deoxytetranucleotide d-pApTpApT and a Sequence-Dependent Model for Poly(dA-dT)

The x-ray structure of the hydrated ammonium salt of the deoxytetranucleotide d-pApTpApT was determined by Patterson and direct methods at a resolution of 1 . The crystal structure contains right-handed double-helical segments formed by complementary Watson-Crick-type hydrogen bonding between the adenine and thymine bases of neighboring molecules. The minihelix contains two base pairs. The chains are antiparallel. The A-T and T-A sequences have different phosphodiester conformations. The deoxyribose-pucker and the sugar-base orientation alternate along the chain depending on the nature of the base ($3^\prime$ -endo for purine and $2^\prime$ -endo for pyrimidine). The extended structure is stabilized by base-base, base-sugar, and hydrogen-bond interactions. The minihelix of two base pairs provides starting coordinates for model-building studies of the dA-dT polymer. A B-DNA-type polymer structure is described, which has sequence-dependent alternations of both the deoxyribose pucker and the phosphate diester bridge conformation. Such sequence-dependent DNA structures, if present locally in regions such as operator sequences, could facilitate sequence-specific interactions. The crystal study also suggests possible geometrical parameters for the replication fork