title: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.
abstract: DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed.
authors: Department of Pathology, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
authors: Jyh Yea
authors: JY
authors: Chia
authors: Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.|Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
authors: Wen Siang
authors: WS
authors: Tan
authors: Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
authors: Chyan Leong
authors: CL
authors: Ng
authors: Institute of Biochemistry, National Chung Hsing University, 250, Guoguang Rd., Taichung City 402, Taiwan.
authors: Nien-Jen
authors: NJ
authors: Hu
authors: Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.|Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
authors: Hooi Ling
authors: HL
authors: Foo
authors: Department of Pathology, Faculty of Medicine and Health Sciences; Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
authors: Kok Lian
authors: KL
authors: Ho
mesh_terms: D000818:Animals; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D018899:CpG Islands; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D059371:DNA, B-Form / Q000737:chemistry*; D025741:HMGA1a Protein / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D051783:Methyl-CpG-Binding Protein 2 / Q000737:chemistry / Q000235:genetics*; D051379:Mice; D009154:Mutation; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000235:genetics; D011485:Protein Binding; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000235:genetics; D015518:Rett Syndrome / Q000235:genetics; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D059371:DNA, B-Form; C497392:MECP2 protein, human; C497393:Mecp2 protein, mouse; D051783:Methyl-CpG-Binding Protein 2; D009711:Nucleotides; D012097:Repressor Proteins; D014867:Water; D025741:HMGA1a Protein; D003596:Cytosine; D004247:DNA