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.