# Finding and folding novel RNA structures

> **NIH NIH R01** · IOWA STATE UNIVERSITY · 2024 · $316,916

## Abstract

PROJECT SUMMARY/ABSTRACT
Investigating the functional aspects of RNA structure is significant as it provides fundamental knowledge of RNA
biology and advances emergent technologies that seek to use, and target, RNA therapeutically. Major obstacles
to such efforts arise from our limited knowledge of the extent of functional RNA structure encoded within human
pathogenic viral genomes. This renewal seeks to advance upon our previous work that developed a
methodological pipeline for structured RNA discovery. This approach divides the discovery process into two
parts: a scanning step, where long sequences are decomposed into overlapping analysis windows from which
structure-related metrics are predicted and a folding step, where consensus structures across overlapping
windows are generated revealing the most sequence-ordered, thermodynamically stable structures (an
indication of an evolved property). Our approach has been very successful at identifying highly ordered and
functional structures across an array of human pathogens, e.g., SARS-CoV-2, where discovered motifs were
used to develop therapeutic leads. Our overarching hypothesis is that many regulatory RNA structures remain
to be found in the highly restricted space of viral genomes and that they can be uncovered using a holistic
research approach that combines computational and experimental methods. In this renewal, our goal is to make
improvements to our discovery pipeline to overcome its current limitations (most significantly to address higher
order RNA structure) and apply it to medically important viral genomes. The outcomes of this proposal will be:
(i) the generation of a robust methodological pipeline for functional RNA 2D and 3D structure discovery; (ii)
insight into novel regulatory features of pathogenic human viruses; and (iii) leads for future work to
therapeutically target RNA structure.

## Key facts

- **NIH application ID:** 10877610
- **Project number:** 2R01GM133810-06A1
- **Recipient organization:** IOWA STATE UNIVERSITY
- **Principal Investigator:** Walter Moss
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $316,916
- **Award type:** 2
- **Project period:** 2019-09-15 → 2028-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10877610

## Citation

> US National Institutes of Health, RePORTER application 10877610, Finding and folding novel RNA structures (2R01GM133810-06A1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10877610. Licensed CC0.

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