# Discovery and development of artificial nucleic acid ligands to probe cellular interactions

> **NIH NIH R35** · HERBERT H. LEHMAN COLLEGE · 2022 · $158,936

## Abstract

Discovery and development of artificial nucleic acid ligands to probe cellular interactions
The regulation followed by measurement of cellular events, such as intercellular communication, receptor-
ligand interactions, and inter-receptor interactions using molecular tools, will expand our understanding of
cellular decision-making mediated by cell surface receptors. Owing to their synthetic nature and compatibility
with a variety of nano-materials, nucleic acid aptamers are well suited as specific recognition probes for
incorporation into such tools. Aptamers are single-stranded DNA/RNA/XNA (X= nonstandard nucleic acid
base) sequences that bind to a specific target with high affinity and specificity. However, because of their low
solubility in aqueous media, purified cell-surface receptors do not make good targets for in vitro screening of
aptamer ligands. Additionally, in response to ligand binding, cell surface receptors act in concert, forming
transient complexes. Such complexes are hard to constitute in artificial buffer systems while maintaining their
native fold. This means that conventional approaches to aptamer-ligand screening may not lead to aptamers
that are translatable. Addressing this need, the Mallikaratchy Lab recently pioneered a technology termed
Ligand-guided Selection or LIGS to identify functional aptamers from a SELEX (Systematic Evolution of
Ligands by EXponential enrichment) library, against known multi-domain cell surface targets in their native
functional state. LIGS uses the same combinatorial library but takes advantage of characteristics inherent to
SELEX. For example, it is known that the iterative process in conventional SELEX is designed to outcompete
low-affinity binders through a competitive process whereby high-affinity binders move through an increasingly
selective process. LIGS exploits this competition between weak and strong binders in a combinatorial library by
introducing a stronger, known high-affinity secondary ligand, e.g., a monoclonal antibody (mAb), against the
target of interest to outcompete and replace highly specific aptamers. These aptamers can recognize their
target receptors in cultured and clinical samples specifically. Building on our initial work on LIGS, the first goal
of this MIRA is to extend the types of interactions utilized in LIGS to naturally induced conformational switches
of membrane proteins of mechanistic/functional interest to discover artificial ligands based on aptamers against
them. The second goal explores chemical interventions to understand aptamer folding using bioorthogonal
approaches, such as click-chemistry, to facilitate proximity mediated intra-molecular cross-linking. Additionally,
we plan to engineer functional aptamer scaffolds to regulate cell-cell and receptor-ligand interactions using
aptamers already identified using LIGS, explicitly focusing on the modulation of TCR-CD3ε in T-cells. A
successful outcome to these goals will result in aptamers able to probe rec...

## Key facts

- **NIH application ID:** 10322671
- **Project number:** 5R35GM139336-02
- **Recipient organization:** HERBERT H. LEHMAN COLLEGE
- **Principal Investigator:** Prabodhika Mallikaratchy
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $158,936
- **Award type:** 5
- **Project period:** 2021-01-01 → 2022-08-25

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10322671

## Citation

> US National Institutes of Health, RePORTER application 10322671, Discovery and development of artificial nucleic acid ligands to probe cellular interactions (5R35GM139336-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10322671. Licensed CC0.

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