Pax-3-DNA interaction: flexibility in the DNA binding and induction of DNA conformational changes by paired domains.

Nucleic Acids Res. 1994 August 11; 22(15): 3131–3137.

PMCID: PMC310286

G Chalepakis, J Wijnholds, and P Gruss

Max-Planck-Institut für Biophysikalische Chemie, Abteilung Molekulare Zellbiologie, Göttingen, Germany.

This article has been cited by other articles in PMC.

Abstract

The mouse Pax-3 gene encodes a protein that is a member of the Pax family of DNA binding proteins. Pax-3 contains two DNA binding domains: a paired domain (PD) and a paired type homeodomain (HD). Both domains are separated by 53 amino acids and interact synergistically with a sequence harboring an ATTA motif (binding to the HD) and a GTTCC site (binding to the PD) separated by 5 base pairs. Here we show that the interaction of Pax-3 with these two binding sites is independent of their angular orientation. In addition, the protein spacer region between the HD and the PD can be shortened without changing the spatial flexibility of the two DNA binding domains which interact with DNA. Furthermore, by using circular permutation analysis we determined that binding of Pax-3 to a DNA fragment containing a specific binding site causes conformational changes in the DNA, as indicated by the different mobilities of the Pax-3-DNA complexes. The ability to change the conformation of the DNA was found to be an intrinsic property of the Pax-3 PD and of all Pax proteins that we tested so far. These in vitro studies suggest that interaction of Pax proteins with their specific sequences in vivo may result in an altered DNA conformation.

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Selected References

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