Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

By Rohit Joshi, J. Passner, R. Rohs, R. Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, A. Aggarwal, Barry Honig, R. Mann. 2007

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Origins of specificity in protein-DNA recognition (2010, positive): “Minor groove-interacting arginines are often presented as part of short sequence motifs that include more than one arginine, such as RQR in Scr (29), RPR in Engrailed (26), RKKR in POU homeodomains (158), and RGHR in MATα2 (144).”
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale (2013, methodology): “Given their importance in DNA shape readout, the predicted features include MGW, Roll, propeller twist (ProT) and helix twist (HelT) (see Supplementary Figure S1 for schematic representations) (3,14,18).”
Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers (2011, background): “Structural modeling has generated important insights into protein-DNA recognition mechanisms, from studies of the relative contributions of direct and indirect recognition (6–8), and the role of DNA shape (9,10) and interfacial waters (11,12) in sequence-specific recognition, to the validity of the ”
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. (2008, neutral): “…context: For instance, the binding specificity of the complex of Drosophila Hox-Exd homeodomain proteins is remarkably different from that of the individual monomers (Joshi et al., 2007), raising the prospect that the monomeric binding preferences may not always be relevant to targeting in vivo.”