# Modular Reagents for Programmable RNA Manipulation by Endogenous Proteins

> **NIH NIH F32** · STANFORD UNIVERSITY · 2024 · $73,828

## Abstract

PROJECT SUMMARY:
New strategies to targeted difficult-to-drug diseases such as cancers, neurodegeneration, and genetic disorders
are urgently needed. RNA manipulation is an emerging, therapeutically attractive paradigm which allows target
intervention orthogonal to drugging proteins and without the permanence of gene editing. A variety of tools for
RNA manipulation have been developed, but they rely on ribonuclear proteins, which are difficult to deliver in
vivo or are limited in scope of effect. This proposal aims to develop RNA-based bifunctional molecules (RBMs)
which will consist of an RNA oligonucleotide liked to a small molecule which recruits an effector protein, and will
enable modular, programmable targeting of RNA with a variety of manipulations. The proposed mechanism for
RBMs is based on small interfering RNA (siRNA) oligonucleotides which are widely used as research tools and
have resulted in multiple approved therapeutics. In cells, siRNAs are loaded into Argonaute (AGO) proteins
which are part of the RNA silencing complex (RISC). AGO then guides RISC to mRNA targets complementary
to its loaded siRNA guide, which are cleaved upon binding, resulting in translational silencing. The
oligonucleotide portion of RBMs will function much like siRNAs but will feature key mismatches with the target
RNA. Such mismatches have been shown to oblate the cleavage activity of RISC while maintaining target
binding. Target binding will induce proximity between the target RNA and an effector protein recruited by the
small molecule ligand of the RBM, allowing the effector to act on the target. I will synthesize a small library of
RBMs with variable linker lengths and positions, and verify that they can interact with AGO and a model effector
protein in vitro (Aim 1). Next, I will use AGO pulldown to show that these interactions can be recapitulated in
cells, then use two model systems to show that RBMs can enable post-transcriptional control of mRNA targets
(Aim 2). Finally, I will show that RBMs targeting nuclear, long non-coding RNAs can enable control of gene
expression (Aim 3). Overall, this will create a platform in which the siRNA paradigm is expanded to enable a
much wider variety of manipulations, which will enable novel research tools and therapies.
 This project will use my existing skills in synthetic chemistry as a foundation and then allow me to branch out
in the field of chemical biology. The laboratory of my sponsor, Prof. Steven Banik, is a supportive research
environment which will enable me to successfully learn the new skills required to execute this proposal. Prof.
Banik is a member of Stanford's Chemistry Engineering and Medicine for Human Health (ChEM-H), a highly
collaborative and interdisciplinary institute. Stanford and ChEM-H will afford me all necessary research
resources, a variety of opportunities for professional development, and the opportunity to work with, and learn
from many, different scientists.

## Key facts

- **NIH application ID:** 10830248
- **Project number:** 5F32GM149057-02
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Robert Follett Lusi
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $73,828
- **Award type:** 5
- **Project period:** 2023-02-27 → 2026-02-26

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10830248

## Citation

> US National Institutes of Health, RePORTER application 10830248, Modular Reagents for Programmable RNA Manipulation by Endogenous Proteins (5F32GM149057-02). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10830248. Licensed CC0.

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