Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition.
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 N6 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 N6-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.
Bae
Sung-Hun
SH
Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejon 305-701, Republic of Korea.
Cheong
Hae-Kap
HK
Cheong
Chaejoon
C
Kang
Sukhyun
S
Hwang
Deog Su
DS
Choi
Byong-Seok
BS
D001425:Bacterial Outer Membrane Proteins; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D019175:DNA Methylation; D004260:DNA Repair; D004268:DNA-Binding Proteins; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins; D007700:Kinetics; D008780:Methyltransferases / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011522:Protons; D014157:Transcription Factors / Q000378:metabolism*
D001425:Bacterial Outer Membrane Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D011522:Protons; C089746:SeqA protein, E coli; D014157:Transcription Factors; D004247:DNA; D008780:Methyltransferases