Figure 1.

Comparison of the structures of 5-hydroxymethylcytosine (^5hmC) and 5-methyl cytosine (^5mC) in DNA Holliday junctions. (A) The crystal structure of the hydroxylmethylated sequence d(CCGGCG₆^5hmC₇C₈GG) is shown with the DNA backbones traced as ribbons (colored gold for the outside continuous strands and green for the junction crossing strands). The ^5hmC bases, along with the phosphate groups that they are H-bonded to, are rendered as ball-and-stick models, with the carbon atoms of the nucleotides along the continuous strand colored gold and those at the junction colored green. The ^5hmC bases on the crossover strands have hydroxyl groups that occupy two rotamer conformations, both shown on the image. (B) The DNA backbone of the methylated sequence d(CCGGCG₆^5mC₇C₈GG) is traced as ribbons (grey along the outside continuous strands and blue along the junction crossing strands). The ball-and-stick models of the ^5mC bases and their interacting the phosphate groups are colored grey on the continuous and blue on the junction crossing strands.