Protein stitchery: Design of a protein for selective binding to a specific DNA sequence
Changmoon Park, Judith L. Campbell, William A. Goddard III
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.
Group Members
Park, C., Campbell, J. L., & III, W. A. G. (1992). Protein stitchery: Design of a protein for selective binding to a specific DNA sequence. *Proc. Natl. Acad. Sci. U.S.A.*, *89*(19), 9094-9096. https://doi.org/10.1073/pnas.89.19.9094