  RNA co-transcriptional folding has long been suspected to play an active role
in helping proper native folding of ribozymes and structured regulatory motifs
in mRNA untranslated regions. Yet, the underlying mechanisms and coding
requirements for efficient co-transcriptional folding remain unclear.
Traditional approaches have intrinsic limitations to dissect RNA folding paths,
as they rely on sequence mutations or circular permutations that typically
perturb both RNA folding paths and equilibrium structures. Here, we show that
exploiting sequence symmetries instead of mutations can circumvent this problem
by essentially decoupling folding paths from equilibrium structures of designed
RNA sequences. Using bistable RNA switches with symmetrical helices conserved
under sequence reversal, we demonstrate experimentally that native and
transiently formed helices can guide efficient co-transcriptional folding into
either long-lived structure of these RNA switches. Their folding path is
controlled by the order of helix nucleations and subsequent exchanges during
transcription, and may also be redirected by transient antisense interactions.
Hence, transient intra- and intermolecular base pair interactions can
effectively regulate the folding of nascent RNA molecules into different native
structures, provided limited coding requirements, as discussed from an
information theory perspective. This constitutive coupling between RNA
synthesis and RNA folding regulation may have enabled the early emergence of
autonomous RNA-based regulation networks.
