Atomic Force Microscopy Measurements and Model of DNA Bending Caused by Binding of AraC Protein

Atomic force microscopy (AFM) was used to conduct single-molecule imaging of protein/DNA complexes involved in the regulation of the arabinose operon of Escherichia coli . In the presence of arabinose, the transcription regulatory protein AraC binds to a 38 bp region consisting of the araI1 and araI2 half-sites. The structure of full-length AraC, when bound to DNA, was not previously known. In this study, AraC was combined with 302 bp and 560 bp DNA and arabinose, deposited on a mica substrate, and imaged with AFM in air. A statistical analysis showed that AraC induces a bend in the DNA with an angle of 69° ± 25°. By using known domain structures of AraC, geometric constraints, and contacts determined from biochemical experiments, we developed a model of the tertiary and quaternary structure of DNA-bound AraC in the presence of arabinose. The DNA bend angle predicted by the model is in agreement with the measurement value. We discuss the results in view of other regulatory proteins that cause DNA bending and formation of the open complex to initiate transcription.