Structure and dynamics of hemimethylated GATC sites Implications for DNA-SeqA recognition

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DNA methylation occurs in most organisms from bacteria to mammals and provides a mechanism for epigenetic control of a variety of cellular processes. In Escherichia coli, most of the N-6 positions in adenines found in the sequence GATC are methylated by DNA adenine methyltransferase. After DNA replication, the GATC sites exist transiently in the hemimethylated state, and the specific recognition of these hemimethylated GATC sites is essential for several processes, including sequestration of the site of replication initiation by the SeqA protein, strand discrimination in DNA mismatch repair by the MutH protein, and transcription of several genes. Here, we characterize the solution structure and dynamics of two dodecamer DNA duplexes that each contains a single GATC site in either unmethylated or hemimethylated state. We found that the N-6-methylated adenine of a hemimethylated GATC site undergoes a slow trans-cis interconversion. The release of a tightly bound cation from hemimethylated DNA explains the instability of this structure. In addition, quantitative structural analysis revealed that hemimethylated DNA has unusual backbone structures and a remarkably narrow major groove. These dynamic and structural features provide insights into the specific recognition of hemimethylated GATC sites by the SeqA protein.
Publisher
AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Issue Date
2003-11
Language
English
Article Type
Article
Keywords

ESCHERICHIA-COLI CHROMOSOME; NUCLEIC-ACID CONFORMATIONS; ADENINE METHYLATION; PROTON-EXCHANGE; DAM METHYLASE; AMINO-GROUPS; REPLICATION; STABILITY; SEQUENCE; INITIATION

Citation

JOURNAL OF BIOLOGICAL CHEMISTRY, v.278, no.46, pp.45987 - 45993

ISSN
0021-9258
URI
http://hdl.handle.net/10203/83621
Appears in Collection
CH-Journal Papers(저널논문)
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