CCAAT-BOX BINDING-PROTEIN NF-Y (CBF, CP1) RECOGNIZES THE MINOR-GROOVEAND DISTORTS DNA

The CCAAT box is one of the most common promoter elements, The evoluti onarily conserved heteromeric factor NF-Y binds this sequence with hig h affinity and specificity. By comparing the methylation interference patterns of different sites, performing electrophoretic mobility shift assays (EMSA) with IC-substituted oligonucleotides and competition ex periments with the minor groove binding (MGB) drugs distamicin A, tall imustine and Hoechst 33258 we show that NF-Y makes key minor groove in teractions, Circular permutation assays on four CCAAT boxes, MHC Class II Ea, HSP70, epsilon-globin and MSV, indicate that NF-Y is able to d istort the double helix by angles of 62-82 degrees, depending on the s ite used, and suggest that nucleotides flanking the CCAAT pentanucleot ide influence the degree of bending.