The crystal structure of N4-methylcytosine-guanosine basepairs in the synthetic hexanucleotide d(CGCGm4CG)

The structure of d(CGCGm4CG) where m4C = N4- methylcytosine has been determined by crystallographic methods. The crystals are multifaced prisms, with orthorhombic space group P212121 and unit cell dimensions of a=17.98, b=30.77 and c=44.75A. The asymmetric unit consists of one duplex of hexanucleotide and 49 waters. The R-factor is 0.189 for 1495 reflections with F ≥ a(F) to a resolution limit of 1.8A. The double helix has a Z-DNA type structure which appears to be intermediate in structure to the two previously characterised structure types for Z-DNA hexamers. The two m4C G base-pairs adopt structures that are very similar to those of the equivalent basepairs in the structure of the native sequence d(CGCGCG) except for the presence of the methyl groups which are trans to the N3 atoms of their parent nucleotides and protrude into the solvent region. The introduction of the modified base-pairs into the d(CGCGCG) duplex appears to have a minimal effect on the overall base-pair morphology of the Z-DNA duplex.