# Discovery of pseudoknots in the SARS-CoVID-2 RNA genome with SNP analysis

> **NIH NIH R35** · PENNSYLVANIA STATE UNIVERSITY, THE · 2020 · $7,605

## Abstract

Abstract
The Bevilacqua lab has contributed to the field of RNA biology through two disparate approaches. One is
rigorous ribozyme mechanism and the other is discovery-based RNA structural genomics. A major goal of the
parent award is to bridge these two areas to discover new RNA biology and to characterize it at the molecular
level. This proposal advances ways to investigate RNA structure and its contribution to the COVID-19
outbreak. We have already computationally identified structural domains in the RNA genome of SARS-CoV-2,
which causes COVID-19, and confirmed these with recent reports on BioRxiv. Uniquely, we identified potential
pseudoknots, which are regions of RNA folding complexity that are typically essential for function. The plan for
the summer is for our undergraduate student Peter Forstmeier to work through the thousands of available
SARS-CoV-2 genomes that contain single nucleotide polymorphisms (SNPs) to identify changes in pseudoknot
strength and RNA folding. SNPs in pseudoknots may lead to changes in the stability of the structure, as so-
called riboSNitches. The effect of these SNPs on pseudoknots may have implications on the spread and
potential virulence of COVID-19. Our hypothesis is that such information will provide targets for therapeutics,
both antisense oligonucleotides and small molecules, which can halt spread of the virus. This administrative
supplement would provide a unique opportunity for Peter to advance his training to pursue his eventual goal of
being a physician-scientist. Because it is computational, it is amenable to working from home during the
pandemic, and we can mentor Peter using videoconferencing. Peter is a rising junior and has already spent a
year in the Bevilacqua lab developing his coding skills and preparing a pipeline to search for novel RNA
structures making him a good fit for this project.

## Key facts

- **NIH application ID:** 10154628
- **Project number:** 3R35GM127064-03S1
- **Recipient organization:** PENNSYLVANIA STATE UNIVERSITY, THE
- **Principal Investigator:** PHILIP C BEVILACQUA
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $7,605
- **Award type:** 3
- **Project period:** 2018-05-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10154628

## Citation

> US National Institutes of Health, RePORTER application 10154628, Discovery of pseudoknots in the SARS-CoVID-2 RNA genome with SNP analysis (3R35GM127064-03S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10154628. Licensed CC0.

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