The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)2

We report the 2.6 Å resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P43. This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating ‘CG’ sequences, and has a ‘TA’ step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair–base pair stacking interactions show alternations at the alternating pyrimidine–purine and purine–pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.

► This is the first tetra-decanucleotide crystallized as A-DNA duplex.
► The alternating sequence shows an alternating pattern of base stacking and twist values.
► These variations reminiscent of the dinucleotide repeat in left-handed Z-DNA.
► Unlike other A-DNA crystal packing, each helix has six different types of contacts with symmetry-related neighbours.