Structure of the B-DNA oligomers d(CGCTAGCG) and d(CGCTCTAGAGCG) in new crystal forms

We present the structure of the dodecamer CGCTCTAGAGCG and the related octamer CGCTAGCG, both in the B form, determined by single crystal X-ray diffraction. Two different crystal forms of the octamer have been obtained, with either three or four duplexes in the asymmetric unit. The dodecamer crystallizes in the P2(1) space group with two duplexes in the asymmetric unit. Very few such structures have been previously reported, while the octamer structure is the first one determined with three duplexes in the asymmetric unit. It is also the first octamer with standard Watson-Crick base pairs to be crystallized in the B form. The crystal structure is stabilized in both cases by interactions between the guanines in the two terminal base pairs of each duplex. This interaction is similar to that found in most dodecamers which have been previously studied, but here it is found in a new unit cell (for the dodecamer) and in one octamer. In the dodecamer cytosine-stacking interactions between neighbor duplexes are also present. The two dodecamer duplexes in the asymmetric unit show different patterns of bending, while the octamer molecule has a rather straight helical axis. The results presented confirm the strong conformational variability of the TA pyrimidine-purine step and demonstrate a clear alternating structure for the (CT/GA)n sequence.