While high-density DNA microarrays have been available for a while, similar RNA microarray technology has proven difficult to achieve, stunting RNA synthesis efforts. Now researchers at the Faculty of Chemistry of the University of Vienna and McGill University have developed an approach to allow RNA to be chemically synthesized about a million times more efficiently than previously possible.
A paper published in Angewandte Chemie International Edition describes the method, made possible by a combination of two key techniques: photolithographic fabrication technology—an etching technique common in the semiconductor chip industry—and the development of a new protecting group.
For the method, biological photolithography was used for the chemical synthesis of RNA. This technique makes it possible to produce RNA chips with a density of up to one million sequences per square centimeter. In this case, the researchers used UV-A light, rather than ultraviolet light that is used for traditional photolithography in the semiconductor chip industry.
The researchers were also able to develop a new protecting group for the RNA 2’-hydroxyl group that is compatible with photolithographic synthesis. Acetyl levulinyl ester (ALE), is the basis of the new group and it gives very high yields in the coupling reactions between the added RNA monomers in the extension of the RNA strand.
"The combination of high-synthesis yield and ease of handling makes it possible to foresee the preparation of longer, and functional, RNA molecules on microchips" said Jory Liétard, post-doc of the group of Mark Somoza.
To show that high-density is feasible with the new method, the researchers developed a complex RNA permutation library with 262144 unique sequences.