RNA-ligand Interaction Analysis

Why RNA-ligand Interaction Analysis?

RNA molecules are not passive carriers of genetic information but active players in cellular processes. They can interact with small molecules, proteins, and other RNA molecules, forming dynamic complexes that regulate gene expression and control cellular functions. Studying RNA-ligand interactions provides a deeper understanding of RNA biology, which can lead to breakthroughs in disease research and the development of novel therapeutics.

Identifying RNA-binding Ligands

RNA-binding ligands are molecules that interact specifically with RNA, modulating its structure and function. By characterizing RNA-ligand interactions, researchers can identify potential RNA-binding ligands, such as small molecules or drugs, which may have therapeutic implications. For example, discovering a small molecule that can selectively bind and modulate the activity of an oncogenic RNA could open new avenues for cancer treatment.

Understanding RNA Structure and Function

RNA molecules possess intricate three-dimensional structures that are essential for their biological functions. Ligands can influence RNA folding, stability, and catalytic activity. Analyzing RNA-ligand interactions allows scientists to gain insights into RNA structure-function relationships, unraveling the molecular basis of RNA-mediated processes.

Unraveling RNA Regulatory Networks

RNA molecules play vital roles in gene regulation by interacting with other RNA molecules, proteins, and ligands. By studying RNA-ligand interactions, researchers can decipher complex regulatory networks, including RNA-RNA interactions and RNA-protein interactions. This knowledge can provide valuable insights into disease mechanisms and identify potential therapeutic targets.

Technology Platform for RNA-ligand Interaction Analysis at Creative Proteomics

Creative Proteomics offers a cutting-edge technology platform for RNA-ligand interaction analysis. This platform combines state-of-the-art techniques and expertise to provide comprehensive solutions for studying RNA-ligand interactions.

1. Cross-linking and immunoprecipitation (CLIP)

CLIP crosslinks RNA molecules to their interacting proteins, followed by immunoprecipitation and sequencing.Creative Proteomics uses CLIP to identify RNA-binding proteins and map their binding sites on RNA molecules to help understand RNA-protein-ligand interactions and their functions.

2. RNA pull-down assay

In this technique, the RNA molecule of interest is biotinylated and incubated with cell or tissue lysates. The RNA-protein complex is then captured with streptavidin beads and analyzed by mass spectrometry or Western blotting. Creative Proteomics offers custom RNA pull-down assays that enable researchers to identify and characterize RNA-binding proteins and their ligands.

3. Isothermal Titration Calorimetry (ITC)

Creative Proteomics uses ITC to directly measure the binding affinity and thermodynamics of RNA-ligand interactions, helping to understand the binding mechanism and providing critical information for drug discovery and optimization.

4. Microscale Thermophoresis (MST)

MST measures the motion of molecules in a temperature gradient that is influenced by their binding to each other. Creative Proteomics uses MST to determine the binding affinity, thermodynamics and kinetics of RNA-ligand interactions.

Measurement of RNA/small molecule interactionsMeasurement of RNA/small molecule interactions (Moon et al., 2018)

5. Surface Plasmon Resonance (SPR)

SPR enables real-time monitoring of biomolecular interactions and analyzes RNA-ligand interactions in a label-free and quantitative manner, providing information on binding kinetics, affinity and specificity.

6. Mass Spectrometry (MS)

Use mass spectrometry-based methods such as affinity purification with mass spectrometry (AP-MS) to identify and characterize RNA-binding proteins and ligands.

7. Fluorescence-based Assays

Fluorescence-based assays are widely employed to study RNA-ligand interactions due to their sensitivity and versatility. Techniques such as fluorescence resonance energy transfer (FRET) and fluorescence polarization (FP) can be utilized to probe the binding of fluorescently labeled RNA molecules to ligands. These assays enable researchers to measure binding affinities, screen for potential ligands, and investigate binding kinetics.

8. RNA-protein Co-immunoprecipitation (RIP)

RIP is a technique used to study RNA-protein interactions in cells or tissues. It involves crosslinking RNA molecules to their associated proteins, followed by immunoprecipitation using specific antibodies against the protein of interest. Creative Proteomics employs RIP to identify RNA-binding proteins and their ligands, shedding light on RNA-protein-ligand interactions and their functional roles.

9. Electrophoretic Mobility Shift Assay (EMSA)

EMSA uses gel electrophoresis to separate RNA-ligand complexes from unbound RNA. By comparing the migration patterns of RNA in the presence and absence of the ligand, the binding affinity and specificity of the interaction can be assessed.

10. Computational Modeling and Analysis

In addition to experimental techniques, Creative Proteomics utilizes advanced computational modeling and analysis to predict and validate RNA-ligand interactions. Molecular docking, molecular dynamics simulations, and machine learning algorithms are employed to gain insights into the binding modes, energetics, and dynamics of RNA-ligand complexes.


  1. Moon, Michelle H., et al. "Measuring RNA–ligand interactions with microscale thermophoresis." Biochemistry 57.31 (2018): 4638-4643.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.