Thymine methyls and DNA–protein interactions

Open Access
Publisher Website
Google Scholar
Abstract
Evidence is summarized showing that thymine methyls are as important in the recognition of specific sequences by proteins as are the more widely recognized hydrogen bonding sites of bases in the major groove (1). Strongest evidence has come from experiments using functional group mutagenesis (2) in which thymines in a specific recognition sequence (e.g., promoters, operators and restriction sites) are replaced by oligonucieotide synthesis with methyl-free uradl or cytosine and 5-methylcytosine. Such experiments have shown that thymine methyls can provide contact points via van der Waals Interactions with amino acid side chains of specific DNA binding proteins. Actual contact between a thymine methyl and carbons of a glutamine side chain has been observed in a cocrystal of the phage 434 repressor and its operator by X-ray analysis. The Issue of why thymine occurs in DNA is discussed in light of these findings.