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Updated: Jun 8, 2026

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
Published on: August 7, 2021
Predicting ribosomal frameshifting efficiency
1Department of Physics and Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA.
Abstract:
Many retroviruses use -1 ribosomal frameshifting as part of the mechanism in translational control of viral protein synthesis. Quantitative prediction of the efficiency of -1 frameshifting is crucial for understanding the viral gene expression. Here we investigate the free energy landscape for a minimal -1 programmed ribosomal frameshifting machinery, including the codon-anticodon base pairs at the slippery site, the downstream messenger RNA structure and the spacer between the slippery site and the downstream structure. The free energy landscape analysis leads to a quantitative relationship between the frameshifting efficiency and the tension force generated during the movement of codon-anticodon complexes, which may occur in the A/T to A/A accommodation process or the translocation process. The analysis shows no consistent correlation between frameshifting efficiency and global stability of the downstream mRNA structure.
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