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

Abstract

The DNA fragment, d(CG) 3, was co-crystallized with N-(3-amino-propyl)- N-(5-aminopropyl)-1,4-diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 × 0.5 × 0.5 mm 3, X-ray intensity data were collected up to 1.0 Å resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG) 3 molecule. The d(CG) 3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG) 3 molecule. Furthermore, the binding modes between d(CG) 3 and thermospermine were different from those of d(CG) 3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG) 3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG) 3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG) 3 molecule and the magnesium cation.