Structures of d(Gm⁵CGm⁵CGCGC) and d(GCGCGm⁵CGm⁵C): effects of methylation on alternating DNA octamers

The crystal structures of two alternating octamers d(Gm⁵CGm⁵CGCGC) and d(GCGCGm⁵CGm⁵C) have been determined at 1.7 and 1.9 Å resolution with R_work/R_free of 16.9/19.6% and 17.9/19.8%, respectively. The two octamers crystallized in the same tetragonal space group P4₃2₁2, with unit-cell parameters a = b = 43.0, c = 24.9 Å and a = b = 43.1, c = 24.7 Å, respectively. Both structures adopt the A-type double helix and the abutting crystal packing. Despite the different positions of the methylated cytosine in the sequence, the two octamers display essentially the same conformation. The close similarity of the two structures indicates that methylation at different positions in a DNA sequence does not affect the helical conformation of the alternating DNA octamer. Investigation of other related crystal structures implies that methylation of cytosine stabilizes the A-type conformation for alternating DNA sequences beginning with a 5'-purine but is beneficial to the Z-type conformation for alternating DNA sequences beginning with a 5'-pyrimidine.