Abstract
Specific interactions between transcription factors and DNA responsive elements are of fundamental importance in understanding how genetic regulatory proteins control gene transcription. Here we have developed a new method of using atomic force microscopy (AFM) to quantitatively study the single molecular specific interaction between ZmDREB1A, a transcription factor from maize, and its DNA responsive element, dehydration-responsive element (DRE) with core sequence A/GCCGAC. It was found that ZmDREB1A bound to both DRE ACCGAC and GCCGAC efficiently. The single molecular interaction forces of ZmDREB1A with DRE A/GCCGAC were determined to be 101 +/- 5 and 108 +/- 3 pN, respectively. The point mutation of ZmDREB1A in its DNA-binding domain or single base substitution of the DRE core sequence greatly reduced the binding affinity, demonstrating the high sensitivity of the AFM measurements. AFM is expected to be a simple, quick, sensitive and reliable method that offers valuable information for the characterization of transcription factors and the identification of their potential DNA responsive elements in functional genomics research.