Engineered zinc finger proteins that respond to DNA modification by HaeIIIand HhaI methyltransferase enzymes

Zinc finger modules are capable of specifically interacting with DNA that c ontains 5-methylcytosine (5-mC) in place of cytosine, suggesting that zinc finger-DNA blinding could be regulated by extrinsic methylation of DNA. Her e, we have used phage display to engineer zinc finger proteins that detect and discriminate DNA methylation by the prokaryotic enzymes HaeIII and HhaI . Ln these systems, zinc finger-DNA complexes are induced by DNA modificati on using the appropriate enzyme, which can therefore act as a switch. To fu rther develop the specificity of the switch, zinc finger discrimination bet ween 5-mC and thymine in DNA sequences is demonstrated despite the presence of the characteristic major groove methyl group that is common to both bas es. Specificity was achieved using a DNA-binding strategy involving synergy between adjacent zinc fingers. We propose that engineered zinc fingers tha t recognise particular DNA modifications, such as sequence-specific DNA met hylation, could be integrated into artificial regulatory circuits for the c ontrol of gene expression and other biological processes. (C) 2000 Academic Press.