GATC motifs may alter the conformation of DNA depending on sequence context and N6-adenine methylation status: possible implications for DNA-protein recognition.
As part of our analysis of the role of a uniquely clustered set of dam methylation sites (the motif GATC) within the origin of DNA replication in Escherichia coli, we have studied the effect of GATCs in various methylation states on the intrinsic curvature of DNA. We have designed a set of DNA linkers and used commercially available linkers containing GATC motifs. The linkers were ligated and the electrophoretic mobility of the resulting multimers in different states of methylation was tested relative to reference fragments. We report that properly phased GATCs in certain sequence environments modulate DNA curvature and that these effects may be enhanced by N6-adenine methylation of the GATCs. These structural alterations may in turn affect DNA-protein interactions, especially those involving proteins that rely on both primary sequence and structure for recognition. We present an example, where introduction of a GATC within an integration host factor (IHF) binding site, which does not alter the consensus sequence, reduces the binding affinity of the protein for the modified site.
Braun Laboratories 147-75, California Institute of Technology, Pasadena 91125, USA.
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P
Polaczek
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Kwan
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JL
Campbell
D000225:Adenine / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000737:chemistry; D034982:Integration Host Factors; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018741:Replication Origin; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000378:metabolism
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D034982:Integration Host Factors; D004247:DNA; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); D000225:Adenine