Percent pull down by anti-5-methyl-C antibody increases with increasing number of methylated CpG sites on the target DNA fragment. A) Average % pull down from multiple experiments using 10 ng/ul of antibody in the IP assays with differently methylated target DNA. Six regions quantitated by the TaqMan assay in five different MseI restriction fragments are presented. The number of CpG sites on each MseI restriction fragment and target DNA methylated with HhaI, HpaII, or SssI methylase harbor different numbers of methylated CpG sites as indicated in Table 1. B) 5 ng/ul of antibody was used in the IP assays. C) Parallel IP assays of A) and B) with no antibody as negative controls. In these three illustrations, the Y-axis is % pull down. D) Plot of methylated CpG sites on the DNA fragment (X-axis) and the % pull down (Y-axis) from the IP assays using 10 ng/ul antibody.