Methyl-CpG binding protein 2 (MeCP2) is a transcriptional regulator and a chromatin-associated structural protein. MeCP2 deregulation results in two neurodevelopmental disorders: MeCP2 dysfunction is associated with Rett syndrome, while excess of activity is associated with MeCP2 duplication syndrome. MeCP2 is an intrinsically disordered protein (IDP) constituted by six structural domains with variable, small percentage of well-defined secondary structure. Two domains, methyl-CpG binding domain (MBD) and transcription repressor domain (TRD), are the elements responsible for dsDNA binding ability and recruitment of the gene transcription/silencing machinery, respectively. Previously we studied the influence of the completely disordered, MBD-flanking domains (N-terminal domain, NTD, and intervening domain, ID) on the structural and functional features of the MBD (Claveria-Gimeno, R. et al. Sci Rep. 2017, 7, 41,635). Here we report the biophysical study of the influence of the remaining domains (transcriptional repressor domain, TRD, and C-terminal domains, CTDα and CTDβ) on the structural stability of MBD and the dsDNA binding capabilities of MBD and ID. The influence of distant disordered domains on MBD properties makes it necessary to consider the NTD-MBD-ID variant as the minimal protein construct for studying dsDNA/chromatin binding properties, while the full-length protein should be considered for transcriptional regulation studies. • MBD-flanking disordered domains (NTD and ID) increase MBD structural stability and dsDNA binding affinity. • MBD-distant domains (TRD, CTDa and CTDb) hardly affect MBD structural stability and dsDNA binding properties. • MeCP2 contains four potential dsDNA binding sites; MBD and ID contain the main sites for dsDNA binding. • NTD-MBD-ID is the minimal construct for dsDNA binding studies, and full-length protein for transcription studies. • NTD-MBD-ID is appropriate for finding molecules recovering/inhibiting dsDNA interaction (Rett syndrome or MDS treatment). [ABSTRACT FROM AUTHOR]