Visualizing a Transcription Factor’s Search for Binding Sites

From the perspective of a transcription factor, finding a specific binding site amounts to finding a proverbial needle (i.e., a short stretch of DNA, often around a dozen genetic letters only) in a haystack (the genome, ranging from millions to billions of letters, depending on the organism). In an Uppsala University study published today in Nature, researchers shed new light on how DNA-binding proteins find their specific binding sites.

Many proteins utilize a process termed facilitated diffusion to accelerate their search. Using this process, a protein undergoes 3D diffusion until it randomly bumps into a DNA molecule. If the site of collision does not correspond to the correct binding site, the protein can then undergo 1D diffusion, meaning it randomly slides back-and-forth along the DNA before unbinding and returning to 3D diffusion. Scientists have long established that the 1D sliding process accelerates the search, but the precise mechanism of 1D sliding has remained unknown.

In order to tackle these questions, the researchers developed new fluorescence microscopy imaging approaches to observe individual transcription factors sliding along the DNA in real time. They also developed a new way of tracking and shooting extremely fast movies of the rapidly sliding protein.

“It’s great that we can push the dynamic observation of bimolecular interactions to the sub-millisecond time scale—this is where the chemistry of life happens,” says co–corresponding author Johan Elf.

The sliding protein turned out not to strictly follow the track given by the helical geometry of the DNA molecule itself. Instead, it was observed to slip out of its track quite frequently by making short hops.

“By hopping, the protein trades thorough scanning for speed, so it can scan DNA faster,” says co–first author Emil Marklund. “This is a really smart choice by the protein, since it will find the target twice as fast using this search mechanism.”