Interaction between the left-handed Z-DNA and polyamine-2: The crystal structure of the d(CG)₃ and spermidine complex

This paper deals with the crystal structure of d(CG)₃-spermidine complex. The DNA fragment, d(CG)₃, was crystallized with N-(2-amino-propyl)- 1,4-diamino-butane, PA(34), spermidine. The results of its X-ray crystallographic analysis showed many intermolecular contacts between d(CG)₃ and spermidine, but the binding mode of spermidine to the d(CG)₃ molecule is different from that of the d(CG)₃ and N-(2-amino-ethyl)-1,4-diamino-butane [PA(24)] complex: a spermidine molecule bound to the d(CG)₃ and its symmetrically related neighboring d(CG)₃ molecules through the water molecules with hydrogen bonds, while one PA(24) molecule connected directly to one d(CG)₃ molecule, but not to its neighboring d(CG)₃ molecule. In the crystal, the d(CG)₃ molecule was the left-handed Z-form, and three magnesium cations and a sodium cation were observed around the d(CG)₃ moiety with different binding modes from the case of the d(CG)₃-PA(24) complex.