Abstract

The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5′ UTR; the reverse complement of the 5′ UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3′ UTR. For eleven of these elements (the stems in SL1–8, reverse complement of SL1–4, FSE, s2m and 3′ UTR pseudoknot), modeling convergence supports the accuracy …

Date

April 6, 2021

Authors

Ramya Rangan, Andrew M Watkins, Jose Chacon, Rachael Kretsch, Wipapat Kladwang, Ivan N Zheludev, Jill Townley, Mats Rynge, Gregory Thain, Rhiju Das

Journal

Nucleic acids research

Volume

49

Issue

6

Pages

3092-3108

Publisher

Oxford University Press