# Direct nanopore detection of modified RNA to probe structure and dynamics

> **NIH NIH R01** · JOHNS HOPKINS UNIVERSITY · 2021 · $740,864

## Abstract

Project Summary:
RNA is perhaps the most versatile molecule in the cell due to its significant contribution to nearly every cellular
process. But we still don’t really understand many aspects of how RNA features, such as nucleotide
modifications and secondary and tertiary structure, work in concert to regulate its many functionalities. The
central dogma of biology tells us that DNA is transcribed to RNA, which then is translated to protein. We
already know that DNA has a complex web of structural organization and covalent modification which provides
transcriptional control. But modifications, splicing, and structure of RNA involve an even more complex
interplay to regulate protein production. Yet without appropriate tools, we cannot explore this world. Here we
propose to leverage the newly developed direct RNA nanopore sequencing platform to directly interrogate
RNA, enabling us to examine modifications to RNA and their interplay with the dynamics of splicing and RNA
structure. Nanopore sequencing directly probes the chemical structure of the molecule in the pore, allowing us
to measure endogenous RNA modifications; but we first need to understand the raw electrical signal data
produced, through the generation of training sets. To explore the dynamics of RNA production and splicing,
we will utilize this toolbox to examine non-canonical nucleotides, e.g. 4sU, that we inject as a metabolic label
for nascent RNA. For structural probing, we will adapt conventional techniques which label unpaired RNA
nucleotides to allow high-throughput examination of complex RNA structure. These tools and analysis
pipelines will grant new insights into mechanisms of transcriptional regulation, as well as their implications for
human disease.

## Key facts

- **NIH application ID:** 10085662
- **Project number:** 5R01HG010538-03
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Winston George Timp
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $740,864
- **Award type:** 5
- **Project period:** 2019-04-22 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10085662

## Citation

> US National Institutes of Health, RePORTER application 10085662, Direct nanopore detection of modified RNA to probe structure and dynamics (5R01HG010538-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10085662. Licensed CC0.

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