RNA Secondary Structures

Hofacker, Ivo L.; Stadler, Peter F.

doi:10.1002/3527600906.mcb.200500009

Cited by 5 publications

(1 citation statement)

References 134 publications

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“…Proper function of an RNA is intimately linked with proper folding of its structure (Doherty and Doudna 2000;Hofacker et al 2006;Kobori and Yokobayashi 2016;Meyer et al 2020), which creates a selective pressure to conserve the structure, including its pseudoknots (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

The Functional RNA Identification (FRID) Pipeline: Identification of Potential Pseudoknot-Containing RNA Elements as Therapeutic Targets for SARS-CoV-2

Forstmeier

Meyer

Bevilacqua

2023

Preprint

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The COVID-19 pandemic persists despite the development of effective vaccines. As such, it remains crucial to identify new targets for antiviral therapies. The causative virus of COVID-19, SARS-CoV-2, is a positive-sense RNA virus with RNA structures that could serve as therapeutic targets. One such RNA with established function is the frameshift stimulatory element (FSE), which promotes programmed ribosomal frameshifting. To accelerate identification of additional functional RNA elements, we introduce a novel computational approach termed the Functional RNA Identification (FRID) pipeline. The guiding principle of our pipeline, which uses established component programs as well as customized component programs, is that functional RNA elements have conserved secondary and pseudoknot structures that facilitate function. To assess the presence and conservation of putative functional RNA elements in SARS-CoV-2, we compared over 6,000 SARS-CoV-2 genomic isolates. We identified 22 functional RNA elements from the SARS-CoV-2 genome, 14 of which have conserved pseudoknots and serve as potential targets for small molecule or antisense oligonucleotide therapeutics. The FRID pipeline is general and can be applied to identify pseudoknotted RNAs for targeted therapeutics in genomes or transcriptomes from any virus or organism.

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Section: Introductionmentioning

confidence: 99%