5. Conclusions
Traditional methods of determining structure have enabled the DD and DBD structures to be determined by X-ray crystallography and NMR spectroscopy, respectively. These techniques, however, could not determine the entire structure of AraC nor the structure of AraC bound to DNA. AFM is capable of imaging bending of DNA for an ensemble of DNA conformations when small proteins such as AraC (63 kDa) are bound to DNA. The bend angle measurements can be used to validate models constructed from biochemical information, geometric constraints, software for rebuilding DNA from bp and step parameters, and positioning using docking software.