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 Å. 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′‐ endo for purine and 2′‐ 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.