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

Abstract

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(CD) 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.