Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot

• DOI: 10.1371/journal.pcbi.1010922
• Publication Date: 2023-02-28T19:50:29Z
• Authors: Luke Trinity; Ian Wark; Lance Lansing; Hosna Jabbari; Ulrike Stege
• Keywords: Pseudoknot; Nucleic acid structure; Translational frameshift; Sequence (biology)

Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV SARS, and SARS-CoV-2 COVID-19, use a mechanism known as −1 programmed ribosomal frameshifting (−1 PRF) to replicate. possesses unique RNA pseudoknotted structure that stimulates PRF. Targeting PRF in impair viral replication can improve patients’ prognoses. Crucial developing these therapies is understanding the of pseudoknot. Our goal expand knowledge structural conformations. Following alignment approach, we identify similarities pseudoknots SARS-CoV-2, SARS-CoV, MERS-CoV. We provide in-depth analysis pseudoknots, reference noteworthy mutated sequences. To better understand impact mutations, insight on pseudoknot sequence mutations their effect resulting structures. introduce Shapify , novel algorithm given an incorporates reactivity (SHAPE) data partial information output secondary prediction within biologically sound hierarchical folding approach. enhances our conformations by providing energetically favourable predictions are relevant structure-function may correlate with efficiency. Applied pseudoknot, unveils previously unknown paths from initial stems By contextualizing work available experimental data, motivate future research aid 3-D modeling pseudoknots.