RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers

RNA aptamers are useful building blocks for constructing functional nucleic acid-based nanoarchitectures. The abilities of aptamers to recognize specific ligands have also been utilized for various biotechnological applications. Solution conditions, which can differ depending on the application, impact the affinity of the aptamers, and thus it is important to optimize the aptamers for the solution conditions to be employed. To simplify the aptamer optimization process, an efficient method that enables re-selection of an aptamer from a partially randomized library is developed. The process relies on RNA-capturing microsphere particles (R-CAMPs): each particle displays different clones of identical DNA and RNA sequences. Using a fluorescence-activated cell sorter, the R-CAMPs that are linked to functional aptamers are sorted. It is demonstrated that after a single round of reselection, several functional aptamers, including the wild-type, are selected from a library of 16 384 sequences. The selection using R-CAMPs is further performed under the solution containing high concentration of ethylene glycol, suggesting applicability in various conditions to optimize an aptamer for a particular application. As any type of RNA clone can be displayed on the microspheres, the technology demonstrated here will be useful for the selection of RNAs based on diverse functions.