Characterization of sequence-specific DNA binding by the transcription factor Oct-1

The DNA-binding domain of the Oct-1 transcription factor, POU, recognizes a defined DNA sequence known as the octamer element to regulate the expression of both general and cell-type-specific genes. The two-part DNA-binding domain partially encircles the DNA to recognize the eight base pairs of the octamer element. We have characterized the binding of Oct-1/POU to an oct amer element using isothermal titration calorimetry. As found for other cognate protein/DNA complexes, the formation of the Oct-1 POU/DNA complex is associated with a large negative heat capacity change, Delta C(p,obs). However, the observed change is much greater than expected by empirical relationships with buried surface area. Supported by data from proteolysis studies on the free and DNA-bound protein, we propose that the discrepancy in heat capacity arises principally from the partial folding of the Oct-1 POU protein upon complex formation. Formation of the Oct-1 POU/DNA complex is strongly dependent on ionic strength, and the detailed quantification of this relationship suggests that six charged contacts are made between the protein and the phosphate groups of the DNA. This agrees with observations from the crystal structure of an Oct-1 POU/DNA complex.