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Published June 1, 1993 | Published
Journal Article Open

Design superiority of palindromic DNA sites for site-specific recognition of proteins: Tests using protein stitchery


Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three dimers--pCC, pCN, and pNN. All three bind specifically to the appropriately rearranged DNA recognition sites for v-Jun: ATGAcgTCAT, ATGAcgATGA, and TCATcgTCAT, respectively (K_d, approximately 4 nM at 4ºC). Results of DNase I footprinting provide strong support for bent recognition helices in leucine zipper protein-DNA complexes. Comparison of the results for pCC and pNN with those for pCN shows the design superiority of palindromic sequences for protein recognition.

Additional Information

© 1993 National Academy of Sciences. Contributed by William A. Goddard III, February 12, 1993. This is contribution no. 8776 from the Division of Chemistry and Chemical Engineering, California Institute of Technology. We thank Prof. Peter Kim for helpful criticisms. This work was supported by a grant from the Department of Energy-Advanced Industrial Concepts Division. The facilities of the Materials and Molecular Simulation Center are also supported by grants from the National Science Foundation-CHE 91-100289), the National Science Foundation-Advanced Computing, the Department of Energy-Chemical Biology, Allied Chemical, Asahi Chemical, Asahi Glass, Chevron, BF Goodrich, BP America, and Xerox.

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Published - PNAS-1993-Park-4892-6.pdf


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