So far, the folding of large RNA molecules has been studied almost exclusively in vitro and conclusions from these studies apply to in vivo conditions still questionable. A first attempt to compare the folding of a small RNA in vitro and in vivo was carried out with the hairpin ribozyme. Another comparison between in vitro and in vivo RNA folding was undertaken with the group I intron of the T4 phage thymidylate synthase (td) gene.
These two examples suggest that there are similarities between in vivo and in vitro folding. However, there are studies that show that RNA folding can be different in vitro and in vivo, , as exemplified by the human telomerase RNA. The formation of the phylogenetically conserved pseudoknot in the 5′ 5 part of this RNA is not observed in vivo. Furthermore, exon mutants of the Tetrahymena pre- rRNA show a 100-fold decrease in self-splicing splicing in vitro, but were fully rescued in vivo when the pre-rRNA rRNA was expressed in Escherichia coli, , suggesting that RNA folding is facilitated in vivo