Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

Sequence-specific high mobility group (HMG) box factors bind and bend DNA v ia interactions in the minor groove. Three-dimensional NMR analyses have pr ovided the structural basis for this interaction. The cognate HMG domain DN A motif is generally believed to span 6-8 bases. However, alignment of prom oter elements controlled by the yeast genes ste11 and Rox1 has indicated st rict conservation of a larger DNA motif, By site selection, we identify a h ighly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we sh ow that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12 , 12, and 10 base pairs, respectively. Footprinting with a deletion mutant of Ste11 reveals a novel interaction between the 3' base pairs of the exten ded DNA motif and amino acids C-terminal to the HMG domain. The sequence-sp ecific interaction of Ste11 with these 3' base pairs contributes significan tly to binding and bending of the DNA motif.