Flash Light From The Nanoworld

With a super-resolution microscopy method, LMU physicists have for the first time been able to visualize all strands of a DNA nanostructure. This may help in the future to optimize their design for novel applications.

DNA origami is a technique that makes it possible to fold DNA strands into complex, nanometer-accurate objects. The method has great potential for numerous applications in biological and biophysical basic research. Among other things, scientists are currently trying to develop working dynamic nanomachines based on DNA origami. Therefore, it is important to precisely characterize the resulting objects in all individual parts. A team led by Ralf Jungmann , Professor of Experimental Physics at LMU and head of the research group Molecular Imaging and Bionano technology at the Max Planck Institute of Biochemistry (Martinsried), has now achieved a decisive breakthrough: Like the researchers in the journal Nature Communications Using super-resolution microscopy, they were able to visualize all the strands of a structure for the first time and show that their assembly is very robust even under different conditions, but the probability of incorporation seems to depend on the position of the strands in the structure.

The DNA origami combines a long, single-stranded DNA molecule with many short strands. These bind at certain points to the long strand and fold it into exactly predetermined shapes. "In our case, the DNA strands self-assemble into a flat, rectangular structure that is currently used in most DNA origami studies," says Maximilian Strauss, along with Florian Schüder and Daniel Haas first author of the paper. Using a super-resolution microscopy method called DNA-PAINT, the scientists were able to directly map the DNA structure in detail. "This allows us to see for the first time how well the object is assembled," says Strauß.

The trick with the super-resolution DNA-PAINT technique is that the short strands of DNA are bound to dyes that are detected when the strand binds to its counterpart. Repeated attachment and setting of these strands creates a kind of blinking signal. "This allows you to calculate a higher resolution from the individual images and to examine the entire object under the microscope," says Strauß. "You can imagine it like this: When you look at a house with two lighted windows, the windows from a distance look like a single source of light. But if someone switches the lights on and off alternately, you can distinguish the two windows. "Another advantage of this method is that researchers can not only pinpoint the position of the DNA strands, but that they also know the specific flashing signal.

The scientists were able to show with the new investigation method that the assembly of the nanostructure is apparently less prone to failure and many parameters - such as the speed of the process - have little influence on it. By adding additional DNA strands, the researchers were able to improve the assembly, but still not all strands were often built, not all possible binding sites occupied. "For the construction of nanomachines, it is therefore advisable to add the individual components in high excess and to select the position of the modifications according to our mapping of the installation efficiency," says Strauß.

The new method now makes it possible to optimize the construction of DNA nanostructures. In addition, scientists believe that the technique has great potential in quantitative structural biology and can directly determine important parameters such as the labeling efficiency of antibodies, cellular proteins or nucleic acids.