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. 1992 Oct 1;89(19):9094–9096. doi: 10.1073/pnas.89.19.9094

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

C Park 1, J L Campbell 1, W A Goddard 3rd 1
PMCID: PMC50071  PMID: 1409607

Abstract

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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