Figure 5.

Selection of zinc fingers to bind all CAn targets. Zinc fingers were selected from the ‘RA’ library to bind all four CAn targets and processed as described in Figure 3 and in the text. In each case, the entropy filtered zinc fingers have been broken into multiple clusters, the largest three of which are shown. The percentage of the total sequences recovered that are included in each cluster is noted to the left. Boxed clusters were identified at low and high stringency. The specificity of candidates that represent these clusters were tested by B1H selection in the context of the three-finger protein using the C-terminal and N-terminal constant fingers (RSANLVR and RSDNLRA) used in the original finger selection. The sequence of the helix for each candidate zinc finger tested is shown under the arrow that points to the resulting specificity. Below each black line, the published helix suggested to bind each of these targets is also shown (67). Candidate proteins using these published helices were assembled and specificities determined.