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Published October 1, 1992 | Published
Journal Article Open

Protein stitchery: Design of a protein for selective binding to a specific DNA sequence


We present a general strategy for designing proteins to recognize DNA sequences and illustrate this with an example based on the "Y-shaped scissors grip" model for leucine-zipper gene-regulatory proteins. The designed protein is formed from two copies, in tandem, of the basic (DNA binding) region of v-Jun. These copies are coupled through a tripeptide to yield a "dimer" expected to recognize the sequence TCATCGATGA (the v-Jun-v-Jun homodimer recognizes ATGACTCAT). We synthesized the protein and oligonucleotides containing the proposed binding sites and used gel-retardation assays and DNase I footprinting to establish that the dimer binds specifically to the DNA sequence TCATCGATGA but does not bind to the wild-type DNA sequences, nor to oligonucleotides in which the recognition half-site is modified by single-base changes. These results also provide strong support for the Y-shaped scissors grip model for binding of leucine-zipper proteins.

Additional Information

© 1992 National Academy of Sciences. Contributed by William A. Goddard III, June 3, 1992. We thank Prof. Mel Simon (California Institute of Technology) for helpful suggestions and discussion and for use of his laboratory resources (funded by National Science Foundation Grant-DMB-90-18536). We also thank Prof. David Eisenberg (University of California, Los Angeles) for helpful comments. This research was supported by a grant from Department of Energy-Advanced Industrial Concepts Division and by funding from the Materials and Molecular Simulation Center of the Beckman Institute. This is contribution number 8547 from the Division of Chemistry and Chemical Engineering.

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