# Development of novel, user-centric technologies for detection and single-molecule analysis of RNA

> **NIH NIH R35** · STATE UNIVERSITY OF NEW YORK AT ALBANY · 2021 · $386,250

## Abstract

Our understanding of RNA and its complex roles in biology is constantly evolving. We know that most of
the genome is transcribed into RNA, but only a small fraction of these transcripts code for proteins. The
functions of the remaining non-coding RNAs are still largely unknown, but increasing evidence points to
important regulatory roles. Thus, there is increasing interest in exploiting RNA for the improvement of
human health, using RNA as potential disease biomarkers, therapeutics, or therapeutic targets. My lab is
focused on developing novel, user-centric technologies for detection and analysis of RNA to accelerate the
pace of discovery in RNA research and ultimate realize the goal of improving human health.
First, we are developing a “smart reagent” for simple, cost effective, and instrument-free RNA detection.
This reagent consists of nanoscale devices that we call DNA nanoswitches. The DNA nanoswitches self-
assemble by DNA hybridization into molecular switches that change conformations upon binding to
molecules of interest. These conformations can be easily identified using one of the most common lab
tools – gel electrophoresis. The result is that users will be able to detect RNA sequences from biological
samples using a one-step reaction. Over the next five years we will optimize these tools for microRNA,
mRNA, long non-coding RNA, and viral RNA.
Second, we are developing methods for high-throughput single-molecule analysis of RNA. This will be
accomplished by continued development of the Centrifuge Force Microscope (CFM) and associated assays
for RNA analysis. The CFM integrates a centrifuge and a microscope to enable thousands of simultaneous
single-molecule experiments as tethered beads are monitored in real time. Importantly, recent
developments in our lab have enabled these experiments to be performed in a standard benchtop
centrifuge, making such experiments user friendly even at the undergraduate level. Over the next five
years, we will develop CFM features and single molecule assays for three distinct projects: 1) mechanisms
of transcription termination, 2) therapeutic ribozyme optimization, and 3) structure/function probing of
a 3’ UTR in mRNA.
These tools will provide new ways for researchers to detect and analyze various RNAs without expensive
equipment or special training. For each of the technology development projects, we have engaged
regional RNA researchers in collaborations to provide materials, biological context, and feedback to
ensure that we are achieving our goals and the having the broadest possible impact.

## Key facts

- **NIH application ID:** 10238117
- **Project number:** 5R35GM124720-05
- **Recipient organization:** STATE UNIVERSITY OF NEW YORK AT ALBANY
- **Principal Investigator:** Ken A Halvorsen
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $386,250
- **Award type:** 5
- **Project period:** 2017-08-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10238117

## Citation

> US National Institutes of Health, RePORTER application 10238117, Development of novel, user-centric technologies for detection and single-molecule analysis of RNA (5R35GM124720-05). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10238117. Licensed CC0.

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