Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates.

ABSTRACT: Programmed -1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that

SUBMITTER: Hsu CF 

PROVIDER: S-EPMC8266650 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature