# Dissecting the folding and dynamic 3D conformational landscapes of functional RNAs by single-particle cryo-EM

> **NIH NIH F32** · UNIVERSITY OF COLORADO DENVER · 2020 · $32,463

## Abstract

Project summary/abstract
RNAs fold into intricate three-dimensional (3D) structures and undergo conformational changes to perform a
myriad of essential biological functions. As such, an important goal for biomedical research it to understand RNA
folding, dissect the dynamic conformational landscape of functional RNAs, and ultimately use this knowledge to
understand RNA biology. Despite decades of research and significant progress, we are far from a predictive
understanding of RNA folding and 3D conformation, stemming from the small number of RNA 3D structures
solved to date and the difficulty of structurally characterizing dynamic functional RNAs using traditional methods.
For example, X-ray crystallography is a powerful tool that provides atomic level information but is limited to
samples that are conformationally homogeneous. NMR can solve 3D structures of dynamic RNAs but is limited
to small specimens that typically fall below the size of fully functional RNAs. Thus, the scientific premise that
underlays this proposal is the critical need for a better understanding of dynamic functional RNA structures,
which can be gained by applying the powerful method of cryo-EM.
Recent developments have turned cryo-EM into a premier structural biology tool and allow visualization of distinct
conformational states under a variety of solution conditions, potentially to high resolution. As such, cryo-EM
promises 3D assessment of RNA folding and conformational landscapes in a way not previously possible.
However, cryo-EM studies of discrete folded RNAs are sparse and most studies have focused on large RNA-
protein complexes or on a single conformational state. I propose to develop a methodology to employ cryo-EM
for the study of RNA folding and for the dissection of dynamic RNA 3D conformations. To accomplish this, I will
use cryo-EM, biochemistry, and chemical probing to answer long-standing questions about two canonical RNA
model systems: group I introns and viral tRNA-like structures (TLS). These RNAs reflect diversity in function,
size, amount of prior knowledge, dynamics, and predicted architecture and will test the applicability of cryo-EM
to solving diverse RNA biological questions. Thus, my studies will have a double impact: They will answer
important questions about these functional RNAs, while providing new techniques for the study of RNA folding
and dynamic RNA conformations. Given the diversity of functional RNAs in nature, the ability to directly visualize
dynamic RNA 3D conformations may spark an explosion in newly solved 3D structures and in our predictive
understanding of RNA folding and conformational dynamics.

## Key facts

- **NIH application ID:** 10068705
- **Project number:** 1F32GM139385-01
- **Recipient organization:** UNIVERSITY OF COLORADO DENVER
- **Principal Investigator:** Steve Bonilla
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $32,463
- **Award type:** 1
- **Project period:** 2020-09-01 → 2021-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10068705

## Citation

> US National Institutes of Health, RePORTER application 10068705, Dissecting the folding and dynamic 3D conformational landscapes of functional RNAs by single-particle cryo-EM (1F32GM139385-01). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10068705. Licensed CC0.

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