Figure 1.

Model of a six zinc-finger–DNA complex. The zinc fingers (numbered F1–F3 and F4–F6) are based on the structure of the three zinc-finger protein Zif268 (3). The six-finger protein was constructed by connecting F3 to F4 by building in the conserved linker sequence TGEKP, represented in magenta, with insightii. The guanine-rich strand, with which most of the base-specific contacts are made, is represented in red (3′-TGCGGGTGCGGCGGGTGCGA-5′). The zinc atoms are represented in yellow. The structure of the modeled linker is similar to that of the natural linker peptides between F1 and F2 (TGQKP) and between F2 and F3 (TGEKP), respectively (with an rmsd of 0.3 Å for backbone atoms). The modeled linker also retains the general position and hydrogen bond characteristics observed for the natural linkers.