Large-scale native preparation of in vitro transcribed RNA

Biophysical studies of RNA require concentrated samples that are chemically and structurally homogeneous. Historically, the most widely used methods for preparing these samples involve in vitro transcription, denaturation of the RNA, purification based on size, and subsequent refolding. These methods are useful but are inherently slow and do not guarantee that the RNA is properly folded. Possible mis-folding is of particular concern with large, complexly folded RNAs. To address these problems, we have developed methods for purifying in vitro transcribed RNAs in their native, folded states. These methods also have the advantage of being rapid and readily scaled to virtually any size RNA or transcription amount. Two methods are presented: the first is an affinity chromatography approach and the second is a weak ion-exchange chromatography approach. Both use equipment and materials readily available to almost any lab and hence should provide flexibility for those seeking alternate approaches to large-scale purification of RNA in the folded state.