Figure 1.

Zinc finger–DNA interactions. (A) A single zinc finger is shown. The four ‘canonical’ (5) contacts are noted with colored stick arrows between the specified positions of the recognition helix. Positions -1–6 of the recognition helix are labeled. The cross-strand canonical contact between position 2 of the helix and the base immediately 3′ to the core 3 bp target is signified by a yellow dashed line. (B) Two zinc fingers are shown that highlight how zinc finger targets can overlap. The contacts from the N-terminal and C-terminal fingers that both specify the same purple base pair are noted with yellow arrows. (C) A three-fingered protein is shown with a 10-bp target. All four canonical contacts from each finger are shown with arrows and cross-strand contacts with dashed arrows. The 3D design is meant to highlight how the zinc fingers wrap around the DNA and bring contacts by distal fingers close together in 3D space. The helix of the central finger is shown as a rainbow to signify that it contains the randomized library positions of the ‘RA’ library processed in this manuscript. The scaffold sequence for the library is given, with the -1–6 positions of each helix underlined, and the randomized positions indicated by ‘X’. Zinc finger structures are modified from (6).