Single molecule analysis of transcription factor-DNA complexes using atomic force microscopy

Transcription of the Escherichia coli genome is under the control of approximately 300 species of transcription factor. However, the regulatory roles remain unidentified for about 100 species of the transcription factor. As an approach to identify their regulation modes, we analyzed the dynamics of DNA-transcription factor interactions using the atomic force microscopy (AFM). Here we examined the DNA-binding mode of two types of transcription factor in the presence and absence of RNA polymerase: a novel growth-specific nucleoid protein Dan (DNA-binding protein under anaerobic growth conditions); and global regulators, CRP (cAMP receptor protein) and Cra (catabolite repressor and activator), for control of transport and metabolism of carbon sources.