The crystal structure of d(GGm⁵CCGGCC): The effect of methylation on A‐DNA structure and stability

We describe the crystal structure of an octameric DNA sequence, d(GGm⁵CCGGCC), at 2.25 Å resolution. The sequence contains one C5‐methylated cytosine per DNA strand. This methylation corresponds to that utilized in vivo by the HaeIII restriction modification system. The present structure is compared to that of the unmethylated octamer solved previously as well as to other A‐DNA crystal structures. It retains the characteristics seen in these other DNA molecules, i.e., reduced base‐pair tilt angles and increased major groove width, indicating that the presence of the methyl groups does not drastically affect the A‐DNA backbone conformation. The position of the methyl groups appears to block the major grove, thus preventing potential sequence‐specific protein interactions. In addition, the presence of these hydrophobic substituents may enhance the overall stability of the A‐DNA conformation.