The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 °C

Several crystal structure analyses of complexes of synthetic polyamine compounds, including N1-(2-(2-aminoethylamino))ethyl)ethane-1,2-diamine PA(222) and N1-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA(2222), and left-handed Z-DNA d(CGCGCG)2 have been reported. However, until now, there have been no examples of naturally occurring polyamines bound to the minor groove of the left-handed Z-DNA of d(CGCGCG)2 molecule. We have found that spermidine, a natural polyamine, is connected to the minor groove of left-handed Z-DNA of d(CGCGCG)2 molecule in a crystalline complex grown at 10 °C. The electron density of the DNA molecule was clear enough to determine that the spermidine was connected in the minor groove of two symmetry related molecules of left-handed Z-DNA d(CGCGCG)2. This is the first example that a spermidine molecule can form a bridge conformation between two symmetry related molecules of left-handed Z-DNA d(CGCGCG)2 in the minor groove.