RNA is a molecule that plays a vital role in the transfer of genetic information from DNA to protein. However, it can also be folded into complex molecular machines, such as the ribosome, that are essential for protein synthesis in cells. Inspired by natural RNA machines, researchers at the Interdisciplinary Nanoscience Center (iNANO) have developed a method called "RNA origami," which enables the design of artificial RNA nanostructures that fold from a single strand of RNA. The technique has numerous applications in medicine and synthetic biology, and its potential is explored in this article.
RNA Origami Technique
RNA origami is a method inspired by the Japanese paper folding art, origami, where a single piece of paper can be folded into a given shape. Similarly, RNA origami enables the design of artificial RNA nanostructures that fold from a single strand of RNA. The method involves the rational design of RNA sequences that can fold into a specific structure by exploiting the base-pairing properties of RNA. The technique has the potential to be used to create intricate nanostructures that can be used in various applications, such as RNA-based medicine.
Cryo-Electron Microscopy
The RNA origami technique was used to design RNA nanostructures, which were characterized by cryo-electron microscopy (cryo-EM) at the Danish National cryo-EM Facility EMBION. Cryo-EM is a method for determining the 3D structure of biomolecules by freezing the sample so quickly that water does not have time to form ice crystals. This means that frozen biomolecules can be observed more clearly with the electron microscope. Images of many thousands of molecules can be converted into a 3D map, which is used to build an atomic model of the molecule. Cryo-EM investigations provided valuable insight into the detailed structure of the RNA origamis, which allowed optimization of the design process and resulted in more ideal shapes.
Discovery of a Slow Folding Trap
Cryo-EM images of an RNA cylinder sample contained two very different shapes. By freezing the sample at different times, it was evident that a transition between the two shapes was taking place. Using the technique of small-angle X-ray scattering (SAXS), the researchers were able to observe this transition in real-time and found that the folding transition occurred after approximately 10 hours. The researchers had discovered a "folding trap" where the RNA gets trapped during transcription and only later gets released. This discovery has the potential to be used to activate RNA therapeutics at the right time and place in the patient.
Construction of a Nanosatellite from RNA
To demonstrate the formation of complex shapes, the researchers combined RNA rectangles and cylinders to create a multi-domain "nanosatellite" shape, inspired by the Hubble Space Telescope. The nanosatellite was designed as a symbol of how RNA design allows us to explore folding space and intracellular space. However, the satellite proved difficult to characterize by cryo-EM due to its flexible properties, so the sample was sent to a laboratory in the US, where they specialize in determining the 3D structure of individual particles by electron tomography, the so-called IPET-method. The RNA satellite was a big challenge, but by using the IPET method, the researchers were able to characterize the 3D shape of individual particles and thus determine the positions of the dynamic solar panels on the nanosatellite.
The Future of RNA Medicine
The investigation of the RNA origamis contributes to improving the rational design of RNA molecules for use in medicine and synthetic biology. A new interdisciplinary consortium, COFOLD, supported by the Novo Nordisk Foundation, will continue the investigations of RNA folding processes by involving researchers from computer the field of RNA origami is a promising area of research with the potential to revolutionize medicine and synthetic biology. The ability to design and create complex RNA nanostructures that can fold into specific shapes opens up new possibilities for drug delivery and cell reprogramming.
The recent discovery of a slow-folding trap in RNA molecules could be particularly significant in the development of RNA-based therapeutics. The ability to control the timing of RNA folding could be used to activate drugs at specific times and locations within the body, improving their effectiveness and minimizing side effects.
The investigation of RNA origamis has already yielded valuable insights into the structure and behavior of RNA molecules. Cryo-electron microscopy and small-angle X-ray scattering are powerful tools for determining the 3D structure of biomolecules and observing their behavior in real-time. The interdisciplinary consortium COFOLD, supported by the Novo Nordisk Foundation, will continue to build on this research by bringing together experts from a range of fields to design, simulate, and measure RNA folding at higher time resolutions.
However, there are still many challenges to overcome before RNA origami can be widely used in medicine and synthetic biology. One major obstacle is the difficulty of characterizing complex RNA nanostructures. Flexible properties and the tendency to aggregate can make it difficult to obtain high-quality structural data. Further research and development will be needed to improve our understanding of these structures and their behavior.
Journal Information: Ebbe Andersen, Structure, folding and flexibility of co-transcriptional RNA origami, Nature Nanotechnology (2023). DOI: 10.1038/s41565-023-01321-6. www.nature.com/articles/s41565-023-01321-6
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