Direct Observation and Analysis of the Dynamics of the Photoresponsive Transcription Factor GAL4

Abstract

Herein, the direct visualization of the dynamic interaction between a photoresponsive transcription factor fusion, GAL4–VVD, and DNA using high-speed atomic force microscopy (HS-AFM) is reported. A series of different GAL4–VVD movements, such as binding, sliding, stalling, and dissociation, was observed. Inter-strand jumping on two double-stranded (ds) DNAs was also observed. Detailed analysis using a long substrate DNA strand containing five GAL4-binding sites revealed that GAL4–VVD randomly moved on the dsDNA using sliding and hopping to rapidly find specific binding sites, and then stalled to the specific sites to form a stable complex formation. These results suggest the existence of different conformations of the protein to enable sliding and stalling. This single-molecule imaging system with nanoscale resolution provides an insight into the searching mechanism used by DNA-binding proteins.