DNA structures play a key role in the construction of nanoarchitectures because they can be cross-linked in many ways with each other and with other molecules. One type of nanoarchitecture is the three-way junctions that are formed at the branch point of three DNA strands. “Three-way DNA junctions can either form fully paired Watson-Crick duplexes or have some unpaired nucleotides at the branch point of the three DNA strands,” said Isabelle Seemann, scientist at the University of Konstanz. The presence of unpaired nucleotides makes it possible for researchers to modify the structure of the three-way junction. In addition to the original open structure, another structure is able to form in which two arms stand at an angle of 180 degrees to each other. This structure is called a “stacked” conformer. The open formation is characterized by a huge degree of flexibility: the DNA arms can move around and arrange themselves at different distances from each other. The stacked formation is very stable; the distances between the arms are clearly defined. 

Seemann has now succeeded in getting the three-way junction to change between the two conformations. This is achieved by inserting an aptamer into the three-way junction. Aptamers are oligonucleic acids or peptide molecules that bind to specific target molecules (ligands), in this case adenosine triphosphate (ATP). “The aptamer then forms a “stem-bulge-stem” structure which has a kind of hollow space in which two ATP ligands can be bound,” Isabelle Seemann explained. This binding triggers the three-way junction’s change in conformation from the open to the stacked form.

Seemann’s research can be used for many applications in the material sciences, analytics and diagnostics. Both the connection of three-way junctions with each other as well as their linkage with other molecules (e.g. gold particles or semiconductor nanoparticles) play a role in these applications. “If several of these nanoparticles are brought into spatial vicinity to each other, energy can be transferred between the particles. This energy transfer heavily depends on the distance of the particles from each other,” said Seemann. By binding these nanoparticles to the arms of three-way junctions, the researchers can specifically control energy transfer by adding ligands: the distance between the particles changes as the junctions switch from the open to the stacked conformation. This principle has the potential to be used to construct materials that react to changes in the environment and can therefore be applied in solar technology or the development of lenses.

Fluoroimmunoassays are based on a similar principle. Immunoassays are methods used to detect substances in blood, serum and urine. The binding of an apatmer that has been inserted into a three-way junction to a specific substance triggers conformational changes in the junction as well as leading to the rearrangement of the particles bound to the three-way junction. In this respect, the connection of several three-way junctions in nanogrids is of great importance. The addition of ligands then not only leads to the conformational change in one junction, but in a number of three-way junctions. If the addition of the ligands triggers effects such as fluorescence, the effect is reinforced as a result of the large number of cross-linked three-way junctions. Such sensors are perfect for application in the field of medicine as they combine several tasks, for example when visualizing defective cells. If a cell carries a protein that is specific for cancer cells, the aptamer can be designed in a way that it specifically binds this protein, thus triggering a conformational change. The defective cell becomes visible and can even be destroyed in a subsequent reaction.

However, sensors are not just of an optical, but also of an electrochemical nature. Using a nanogrid for producing a material that changes its conductivity as the condition (ligands) changes can therefore be envisaged. This would enable the diagnostic detection of specific substances, for example in drug screening. Such electronic components can also be used as biological transistors for the production of biological computers. To this end, developers will make use of the huge storage capacity of DNA, which stores the entire genetic information in just four bases, for the development of powerful computers. Up until now, researchers have successfully produced different circuits and logic gates from DNA. The assembly of such structures into larger ones that react to a specific input (in this case ATP) with a corresponding output (in this case a conformational change/circuit) is an important step towards developing biological computers.

Much research is still necessary in order to fully exploit Isabelle Seemann’s findings in practice. Over the next few years, Isabelle Seemann is aiming to obtain further insights into DNA structures: “My main area of interest is unconventional DNA structures, where they are found in nature and what their function is. I am also interested in the application of such structures in the field of nanobiotechnology. We’ve only just scratched the surface and I know that a lot of research is still needed,” said Seemann.