To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element.

ABSTRACT: The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable

SUBMITTER: Schlick T 

PROVIDER: S-EPMC8315264 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature