Electrostatic Effects in DNA Bending by GCN4 Mutants

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Abstract
DNA architecture has been shown to be important for cellular processes such as activation of transcription, recombination, and replication. Many proteins reconfigure the shape of duplex DNA upon binding. Previous experiments have shown that some members of the eukaryotic bZIP family of DNA binding proteins appear to bend DNA, while others do not. We are exploring the role of electrostatic effects in DNA bending by bZIP proteins. The yeast bZIP transcription factor GCN4 does not induce DNA bending in vitro. Previously we substituted basic residues for three neutral amino acids in GCN4 to produce a GCN4 derivative that bends DNA by ∼15°. This result is consistent with a model of induced DNA bending wherein excess positive charge in proximity to one face of the double helix neutralizes local phosphate diester anions resulting in a laterally-asymmetric charge distribution along the DNA. Such an unbalanced charge distribution can result in collapse of the DNA toward the neutralized surface. We now present a more comprehensive analysis of electrostatic effects in DNA bending by GCN4 derivatives. It is shown that the direction and extent of DNA bending by these derivatives are a linear function of the charges of the amino acids adjacent to the basic domain of the protein. This relation holds over the charge range +6 (16° bend toward the minor groove) to −6 (25° bend toward the major groove).