Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins.

• DOI: 10.1073/pnas.90.6.2256
• Publication Date: 2006-05-31T12:41:16Z
• Authors: J R Desjarlais; J M Berg
• Keywords: Dissociation constant; Protein design; Sequence (biology); Zinc finger nuclease

We have designed three zinc-finger proteins with different DNA binding specificities. The design strategy combines a consensus framework sequence previously characterized recognition regions such that the specificity of each protein is predictable. first consists identical zinc fingers, which was expected to recognize subsite GCG. This binds specifically 5'-GCG-GCG-GCG-3' dissociation constant approximately 11 microM. second has fingers predicted preferred subsites. site 5'-GGG-GCG-GCT-3' 2 nM. Furthermore, selection experiments indicate this optimal site. A permuted version also constructed and shown preferentially corresponding 5'-GGG-GCT-GCG-3' over non-permuted These results earlier observations on can be extended generalized structures realize use for site-specific proteins. consensus-based system provides useful model study details zinc-finger-DNA specificity.