ROLE OF ASYMMETRIC PHOSPHATE NEUTRALIZATION IN DNA BENDING BY PU.1

The PU.1 transcription factor is a member of the Ets family of DNA bin ding proteins, PU.1 binds to DNA via a loop-helix-loop domain and func tions in the differentiation of hematopoietic cells, The structure of a PU.1-DNA complex was recently reported (Kodandapani, R., Pio, F., Ni , C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R., and Ely, K. (1996) Nature 380, 456-460). The DNA in this complex is deformed by 8 degrees as it curves around the protein, The pattern of electrostat ic contacts between PU.1, and its DNA binding site suggests that later ally asymmetric phosphate neutralization accompanies PU.1 binding, Bec ause of our previous studies showing that such neutralization can indu ce bending in naked DNA, we have explored the effect of phosphate neut ralization by substituting neutral methylphosphonate internucleoside l inkages at relevant positions within DNA containing the PU.1 binding s equence, Consistent with the prediction that DNA will collapse toward its partially neutralized surface, DNA neutralized at seven positions to simulate PU.1 binding is observed to bend by 28 degrees. The direct ions of DNA curvature are slightly different in the co-crystal versus the partially neutralized duplexes, The electrostatic component of the binding energy appears more than enough to account for the DNA bendin g observed in the PU.1-DNA complex.