The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs [1]. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair [1]. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase [2].

1: Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nan X, Meehan RR, Bird A; Nucleic Acids Res 1993;21:4886-4892. PMID:8177735

2: A mammalian protein with specific demethylase activity for mCpG DNA. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M; Nature 1999;397:579-583. PMID:10050851