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Updated: Sep 10, 2026

Peptide-based Identification of Functional Motifs and their Binding Partners
Published on: June 30, 2013
Expanding the DNA-recognition repertoire for zinc finger proteins beyond 20 amino acids
1Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
Abstract:
The design of DNA binding domains based on the Cys2His2 zinc finger motif has proven to be a successful strategy for the specific recognition of novel DNA sequences. Although considerable effort has been devoted to the generation of zinc finger proteins with widely varying DNA-binding preferences, only a limited number of potential DNA binding sites have been targeted with a high degree of specificity. These restrictions on zinc finger design appear to be a consequence of the limited repertoire of side-chain lengths and functionalities available with the 20 proteinogenic amino acids. To demonstrate that these limitations can be overcome through the use of "unnatural" amino acids, expressed protein ligation was employed to incorporate the amino acid citrulline into a single position within a three-zinc finger protein. As anticipated, the resulting semisynthetic protein specifically recognizes adenine in the appropriate position of its binding site.
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