Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer.

ABSTRACT

As insights into RNA's many diverse cellular roles continue to be gained, interest and applications in RNA self-assembly and dynamics remain at the forefront of structural biology. The bifurcation of functional molecules into nonfunctional fragments provides a useful strategy for controlling and monitoring cellular RNA processes and functionalities. Herein we present the bifurcation of the preexisting Spinach aptamer and demonstrate its utility as a novel split aptamer system for monitoring RNA self-assembly as well as the processing of pre-short interfering substrates. We show for the first time that the Spinach aptamer can be divided into two nonfunctional halves that, once assembled, restore the original fluorescent signal characteristic of the unabridged aptamer. In this regard, the split-Spinach aptamer is represented as a potential tool for monitoring the self-assembly of artificial and/or natural RNAs.