Researchers are folding RNA into squares and cylinders and even creating nanoscale versions of the Hubble Space Telescope. A researcher says that RNA origami also enables researchers to design completely new types of effective RNA medicine.
Researchers in RNA nanotechnology are getting better and better at designing exactly what they want from life’s smallest building blocks.
Researchers have now developed a method for designing RNA nanostructures. The RNA origami method enables researchers to shape RNA strands into cylinders, boxes and nanoscale versions of the Hubble Space Telescope in the same way as paper origami.
However, the method was developed for a serious purpose: pushing the limits of the possible and very precisely making medicines with very specific effects in the body.
“RNA medicine is rapidly expanding, and this especially applies to the mRNA vaccines developed in connection with the COVID-19 pandemic. But RNA medicines are also being developed that switch various genes on and off to thereby affect health and disease. We can use RNA origami to make RNA nanostructures that have a more specific effect on the body or that only are effective in one specific place in the body rather than everywhere,” explains a researcher involved in developing RNA origami, Ebbe Sloth Andersen, Associate Professor, Interdisciplinary Nanoscience Center (iNANO), Aarhus University.
The research has been published in Nature Nanotechnology.
Nature is researchers’ best tool
In RNA origami, researchers take advantage of the fact that strands of RNA fold up automatically and form structures based on the sequence of the molecular building blocks.
An RNA strand has only four of these molecular building blocks (nucleotides): adenine, guanine, cytosine and uracil.
The sequence of these four nucleotides causes the RNA strand to fold in on itself in completely predetermined angles and shapes, and the researchers use this to fold the RNA strands into precise three-dimensional shapes.
“Nature is our basic tool. As long as we put the nucleotides together in the right order, the RNA strands form the structure that we want. It can be boxes, cylinders or more complex shapes, but it can also be shapes with specific therapeutic properties,” says Ebbe Sloth Andersen.
A computer program for designing RNA strands
The difficult part of RNA origami is figuring out how the nucleotides have to be located in one long row in an RNA strand for them to automatically fold up and form, for example, a small nanoscale satellite shape.
To achieve this, the researchers developed a computer program that based on how the various nucleotides interact with each other can transform a blueprint of a three-dimensional structure into an RNA sequence that will naturally fold up and form the designed structure.
“Our computer program uses thermodynamic algorithms that find the optimal sequence to form a given structure. Once the software has calculated what the RNA sequence should look like, we send the template to a company that assembles a DNA strand according to our instructions and we can then transcribe this into RNA in the laboratory by using an RNA polymerase,” explains Ebbe Sloth Andersen.
RNA folds surprisingly slowly
Ebbe Sloth Andersen and colleagues carried out several experiments to determine how the sequence on an RNA strand produces a specific three-dimensional structure. Many experiments used cryogenic electron microscopy, which can precisely map molecular structures.
In this way, the researchers could determine what an RNA strand, that according to the computer model should fold into a given structure, actually ends up looking like.
The researchers have also used other techniques, including small-angle X-ray scattering (SAXS), which can measure structural changes in real time in connection with the RNA folding.
Detailed SAXS analysis of an RNA cylinder, that the researchers had designed, showed that their final RNA structure was caught in a kinetic folding trap that forms during folding and was only released after 10 hours.
According to Ebbe Sloth Andersen, this was a big surprise, since RNA normally folds in less than 1 second.
Developing new forms of medicine and vaccines
RNA origami can be used for more than making cylinders, boxes and satellite shapes, which are not visible to the naked eye anyway. Ebbe Sloth Andersen says that RNA origami enables researchers to design RNA medicines that can be used to combat many diseases.
The problem with using RNA in medicine today is that targeting various tissues in the body is very difficult, since the medicine mostly ends up in the liver anyway if the immune system has not already broken it down.
Ebbe Sloth Andersen envisions that specific and unique folding of RNA may enable researchers to send RNA to the place where it is needed, such as organs, the immune system or even the brain. Chemically modifying the RNA medicine so it does not break down as soon as it is injected may also be possible.
The discovery of an RNA folding trap presents interesting pharmaceutical opportunities, since researchers hope to exploit this kind of mechanism to activate RNA drugs at the right time and place in the body.
“RNA can have a pharmaceutical effect in various ways. It can be used to activate the immune system, as with the mRNA vaccines against COVID-19. But RNA can also turn genes on or off, regulate how RNA is cut and spliced in splicing processes or have a pharmaceutical function as a template for making proteins,” concludes Ebbe Sloth Andersen.
The researchers will continue to investigate the development of mRNA vaccines, which are only activated in the right place in the body and thus directly affect the immune cells – thereby enabling a lower dose of RNA medicine and avoiding side-effects.