Systems and Methods for Designing RNA Nanostructures + RNAMake software

Stanford inventors from Professor Rhiju Das's lab have developed a method to optimize nucleic acids, including aptamers and messenger RNAs to be more effective in clinical settings. Aptamers were discovered in the early 1990's but have been difficult to bring to clinical uses due to the necessity of high concentrations to be effective and to expensive modifications needed to ensure chemical stability. These inventors have been able to stabilize and optimize existing aptamers to have tighter binding to their targets and increased stability to degradation in complex biological environments. This is achieved through the computational design of three-dimensional scaffolds that lock aptamers into their desired, binding-ready conformations remarkably, folding RNAs into these three-dimensional structures imparts resistance to cleavage and unwinding by ribonucleases, leading to notably improved chemical and biological stability. Finally, this technology allows for the stabilization of small-molecule binding RNAs with tertiary contacts to improve on the binding of the aptamers and improving fluorescence.