Tertiary Base Triple Formation in the SRV-1 Frameshifting Pseudoknot Stabilizes Secondary Structure Components

• DOI: 10.1021/acs.biochem.0c00611
• Publication Date: 2020-11-09T22:13:46Z
• Authors: Lixia Yang; Desiree-Faye Kaix...; Manchugondanahall...; Zhensheng Zhong; Yiyao Liu; Shaomeng Wang; Yubin Gong; Gang Chen
• Keywords: Pseudoknot; Translational frameshift; Stem-loop; Duplex (building)

Minor-groove base triples formed between stem 1 and loop 2 of the simian retrovirus type (SRV-1) mRNA frameshifting pseudoknot are essential in stimulating −1 ribosomal frameshifting. How tertiary triple formation affects local stabilities secondary structures (stem 2) thus efficiency is not well understood. We made a short peptide nucleic acid (PNA) that expected to invade SRV-1 by PNA–RNA duplex mimic unwinding process translating ribosome. In addition, we used PNA for invading pseudoknot. Our nondenaturing polyacrylamide gel electrophoresis data binding mutants reveal mutations disrupting result enhanced invasion both PNAs. suggest 1–loop interactions can stabilize structural components, 2. Stem stability coupled triples, mediated through long-range effect. The apparent dissociation constants PNAs positively correlated with mechanical efficiencies. relatively simple experiment may be characterize energetic contribution ligand many other RNA DNA structures.