Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Deconvoluting the recognition of DNA shape from DNA sequence

In previous work (Slattery et al; Joshi et al) we described the importance of the three dimensional structure of the DNA double helix – DNA shape – in the recognition of DNA binding sites by the Hox family of transcription factors. In particular, we found that local minima in the width of the DNA minor groove create electronegative pockets that are binding sites for amino acids with positively charged side chains such as arginine. Moreover, our data argued that DNA shape is a consequence of DNA sequence, and thus lead to the idea that the recognition of specific DNA sequences by DNA binding proteins is mediated by both base readout, typically in the major groove, and shape readout (Rohs, et al.). The relationship between DNA shape and DNA sequence leads to a logical loop that is difficult to tease apart: if shape is a consequence of sequence, then is the recognition of a binding site by a transcription factor mediated by the sequence of base pairs or by the resulting shape of the DNA molecule? One prediction of the shape recognition model is that if the shape-detecting amino acids are mutated the shape of the preferred binding sites would become less important. We tested this prediction by mutating the basic residues of Hox proteins known to insert into narrow regions of the DNA minor groove and carrying out in vitro SELEX-seq experiments. Consistent with the importance of DNA shape recognition by this family of homeodomain proteins, we found that DNA molecules selected to bind these mutants had a much smaller propensity to have local minor groove width minima compared to DNA molecules selected to bind the wild type proteins. Further, we were able to transfer the shape recognition properties of one Hox protein to another Hox protein by introducing residues that bind to narrow minor grooves. Together, these findings argue that the recognition of DNA shape is a key aspect of binding site selection by this family of DNA binding proteins.


  1. Joshi R, et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131, pp. 530-543.
  2. Slattery M, et al. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147, pp. 1270-1282.
  3. Rohs R, et al. (2010). Origins of specificity in protein-DNA recognition. Annu Rev Biochem 79:233–269

Namiko Abe1
Matthew Slattery1
Iris Dror2
Remo Rohs2
Barry Honig1
and Richard S. Mann1

1Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10032
2Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089