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Table 7 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

Experimental Approach 3
DNA Target sequence 5’ – 3’ DNA sub-site position w.r.t to F1, F2, F3 Corresponding Helix IHBE score for experimental DNA target and corresponding Helix
GGG Jamieson et al. 1996 [32] GGG 1 RER 0.0
Segal et al. 1999 [45] GGG 2 RHR 39.3
Van et al. 2004 [46] GGG 3 RHR 50.63
GCG Hurt et al. 2003 [44] GCG 1 RER 30.9
Van et al. 2004 [46] GCAGCGGAG 2 RER 21.64
Kim et al. 2010 [43] GCGGGGGCG 3 RER 28.6
GTG Jamieson et al. 1996 (32) GTG 1 RER 1.35
Hurt et al. 2003 [44] GCGGTGGCG 2 RER 19.59
Van et al. 2004 [46] GTGGACGAA 3 RAR 5.5
GAC Rebar et al. 2002 [39] GGGGGTGAC 1 DNR 2.04
Holmes et al. 2005 [40] GTGGACGAA 2 DNR 4.033
Bae et al. 2003 [41] GAC 3 CNR 7.23
  1. In Approach 3, GGG and GAC, show highest affinity with the respective protein sequence when present at a position against Finger 3, whereas GCG and GTG show high affinity for corresponding helix reported from literature for its position against Finger 1 and Finger 2 respectively