Microscopy: vertical DNA in motion

For fundamental processes of life such as the replication, transcription, and repair of DNA, the complex interplay between DNA and proteins plays a decisive role. A team led by LMU chemist Professor Philip Tinnefeld has developed a new fluorescence microscopy method that is capable of visualizing dynamic changes in the structure of DNA and its interaction with proteins at a spatial resolution down to the angstrom range and with a temporal resolution of under a second.

To this end, the researchers exploited a combination of two effects. Firstly, they were able to measure the distance of a dye molecule to a graphene surface, because the dye appears darker – or has a shorter fluorescence lifetime – the closer it is to the graphene. Secondly, they managed to immobilize the DNA on the graphene in such a way that the DNA strands were arranged vertically.

“This allowed us to know the spatial orientation of the DNA during measurements,” explains Tinnefeld. From the changes in brightness of the dye, the researchers can then identify structural changes in the DNA or the movements of proteins along the DNA. “This can decisively advance the analysis of fundamental processes such as DNA repair mechanisms and other important applications,” says Tinnefeld. “Our method has the potential to develop into a widely used technology and open up new opportunities in structural biology and for biosensor systems and related 2D materials.”

A.M. Szalai, G. Ferrari, L. Richter et. al: Single-Molecule Dynamic Structural Biology with Vertically Arranged DNA on a Fluorescence Microscope. Nature Methods 2024