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Table 6 Effect of DNA sub-sites (3-bp) position on the zinc finger binding specificity

From: Exploiting the recognition code for elucidating the mechanism of zinc finger protein-DNA interactions

Target codona
5’- 3’
Haddock scores for different positions of the codon in a 9bp target
F3 F2 F1
GAT −134.49 −131.98 −137.56
GCA −153.31 −130.95 −137.59
GGT −146.3 −136.62 −140.01
  1. aPreference of these DNA sub-sites from Qiang et al. 2002 [17]
  2. GAT shows best binding when present against position Finger 1 of the zinc finger mutant, followed by F3 and F2. However, the 3bp DNA sequences GCA and GGT, show highest affinity to the respective protein sequence with respect to its position against Finger 3 respectively. These DNA mutations have been introduced in the wild type 9bp DNA sequence (5’ GCG TGG GCG 3’) binding to the prototype Zif-268. Hence the positional preference in approach 1 (consensus amino acid and modular binding mode) and 2 (consensus amino acids and synergistic binding mode) follow a similar trend as described