Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors

Abstract—A large fraction of known transcription factors form 2:1 complexes with DNA. In our studies of the assembly of such ternary (protein–protein–DNA) complexes formed by bZIP and bHLHZip proteins, we found that the proteins recognize DNA as monomers. Here we show that protein monomer–DNA complexes are favored at high DNA concentrations. Further, we show that, due to fast rates of association with protein monomers, DNA and other polyanions accelerate the rate of protein dimer formation. Finally, we find that DNA-assisted formation of protein dimers provides a mechanism by which dimeric transcription factors can rapidly discriminate between specific and nonspecific sites. # 2001 Elsevier Science Ltd. All rights reserved