Beyond the "recognition code": Structures of two Cys(2)His(2) zinc finger/TATA box complexes

Background: Several methods have been developed for creating Cys(2)His(2) z inc finger proteins that recognize novel DNA sequences, and these proteins may have important applications in biological research and gene therapy. In spite of this progress with design/selection methodology, fundamental ques tions remain about the principles that govern DNA recognition. One hypothes is suggests that recognition can be described by a simple set of rules-esse ntially a "recognition code"-but careful assessment of this proposal has be en difficult because there have been few structural studies of selected zin c finger proteins. Results: We report the high-resolution cocrystal structures of two zinc fin ger proteins that had been selected (as variants of Zif268) to recognize a eukaryotic TATA box sequence. The overall docking arrangement of the finger s within the major groove of the DNA is similar to that observed in the Zif 268 complex. Nevertheless, comparison of Zif268 and the selected variants r eveal significant differences in the pattern of side chain-base interaction s. The new structures also reveal side chain-side chain interactions (both within and between fingers) that are important in stabilizing the protein-D NA interface and appear to play substantial roles in recognition. Conclusions: These new structures highlight the surprising complexity of zi nc finger-DNA interactions. The diversity of interactions observed at the p rotein-DNA interface, which is especially striking for proteins that were a ll derived from Zif268, challenges fundamental concepts about zinc finger-D NA recognition and underscores the difficulty in developing any meaningful recognition code.