The term ‘DNA origami’ refers to a method for the design and self-assembly of complex molecular structures with nanometer precision. The technique exploits the base-pairing interactions between single-stranded DNA molecules of known sequence to generate intricate three-dimensional nanostructures with predefined shapes in arbitrarily large numbers.
The method has great potential for a wide range of applications in basic biological and biophysical research. Thus researchers are already using DNA origami to develop functional nanomachines. In this context, the ability to characterize the quality of the assembly process is vital.
Now a team led by Ralf Jungmann, Professor of Experimental Physics at LMU Munich and Head of the Molecular Imaging and Bionanotechnology lab at the Max Planck Institute for Biochemistry (Martinsried), reports an important advance in this regard.
In the online journal Nature Communications (“Quantifying absolute addressability in DNA origami with molecular resolution”), he and his colleagues describe a mode of super-resolution microscopy that enables all the strands within these nanostructures to be visualized individually. This has allowed them to conclude that assembly proceeds in a robust fashion under a wide range of conditions, but that the probability that a given strand will be efficiently incorporated is dependent on the precise position of its target sequence in the growing structure.
DNA origami structures are essentially assembled by allowing one long single-stranded DNA molecule (the ‘scaffold’ strand) to interact in a controlled, predefined manner with a set of shorter ‘staple’ strands. The latter bind to specific (‘complementary’) stretches of the scaffold strand, progressively folding it into the desired form.
“In our case, the DNA strands self-assemble into a flat rectangular structure, which serves as the basic building block for many DNA origami-based studies at the moment,” says Maximilian Strauss, joint first author of the new paper, together with Florian Schüder and Daniel Haas.