RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins

A large number of ribonucleoprotein (RNP) complexes are being discovered mediating numerous cellular functions. To investigate the composition, structure, and functional mechanism of RNP complexes, it is advantageous to isolate an RNP that was assembled in vivo. This review provides a systematic overview of a versatile and highly effective method to accomplish this task, namely, the purification of RNPs from cells using genetically encoded RNA aptamers. Inserting an RNA aptamer into the RNA of an RNP enables binding of the tagged RNP with high affinity and specificity to a ligand as an effective affinity chromatography purification strategy. Therefore, the purification of RNPs using aptamers has been used successfully to identify heterogenous populations of RNPs forming around a single RNA as well as to characterize intermediates in the formation of complex RNPs such as the ribosome. Here, we discuss in detail the selection of an appropriate RNA aptamer based on the properties of both the aptamer and its ligand, and we describe critical considerations in designing RNP purifications.