CCAAT-box binding protein NF-Y (CBF, CP1) recognizes the minor groove and distorts DNA

The CCAAT box is one of the most common promoter elements. The evolutionarily conserved heteromeric factor NF-Y binds this sequence with high affinity and specificity. By comparing the methylation interference patterns of different sites, performing electrophoretic mobility shift assays (EMSA) with IC-substituted oligonucleotides and competition experiments with the minor groove binding (MGB) drugs distamicin A, tallimustine and Hoechst 33258 we show that NF-Y makes key minor groove interactions. Circular permutation assays on four CCAAT boxes, MHC Class II Ea, HSP70, ε-globin and MSV, indicate that NF-Y is able to distort the double helix by angles of 62-82°, depending on the site used, and suggest that nucleotides flanking the CCAAT pentanucleotide influence the degree of bending.