A/T run geometry of B-form DNA is independent of bound Methyl-CpG binding domain, cytosine methylation and flanking sequence

Jyh Yea Chia, Wen Siang Tan, Chyan Leong Ng, Nien Jen Hu, Hooi Ling Foo, Kok Lian Ho

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Article number31210
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 9 Aug 2016

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B-Form DNA
Cytosine
Methylation
Methyl-CpG-Binding Protein 2
DNA
DNA Methylation
X-Rays
Rett Syndrome
Water
Differential Scanning Calorimetry
Circular Dichroism
Freezing
Methyl CpG Binding Domain
Salts
Temperature

ASJC Scopus subject areas

  • General

Cite this

A/T run geometry of B-form DNA is independent of bound Methyl-CpG binding domain, cytosine methylation and flanking sequence. / Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien Jen; Foo, Hooi Ling; Ho, Kok Lian.

In: Scientific Reports, Vol. 6, 31210, 09.08.2016.

Research output: Contribution to journalArticle

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