Role of Asymmetric Phosphate Neutralization in DNA

The PU.1 transcription factor is a member of the Ets family of DNA binding proteins. PU.1 binds to DNA via a loop-helix-loop domain and functions 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° as it curves around the protein. The pattern of electrostatic contacts between PU.1, and its DNA binding site suggests that laterally asymmetric phosphate neutralization accompanies PU.1 binding. Because of our previous studies showing that such neutralization can induce bending in naked DNA, we have explored the effect of phosphate neutralization by substituting neutral methylphosphonate internucleoside linkages at relevant positions within DNA containing the PU.1 binding sequence. 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°. The directions 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 bending observed in the PU.1-DNA complex.