GATC motifs may alter the conformation of DNA depending on sequence context and N6-adenine methylation status: Possible implications for DNA-protein recognition

P. Polaczek, Kelvin Kwan, J. L. Campbell

Research output: Contribution to journalArticle

33 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)488-493
Number of pages6
JournalMolecular and General Genetics
Volume258
Issue number5
DOIs
StatePublished - Jul 28 1998
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

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