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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Jun 27, 2025

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries.

Ryosuke Nagasawa^1,2, Kazumitsu Onizuka^3,4,5, Kaoru R Komatsu⁶

¹Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.

Communications Chemistry

|May 1, 2024

Summary

A new system enables large-scale analysis of small molecule-RNA interactions, profiling binding landscapes and facilitating the discovery of novel RNA-binding molecules for targeted therapies.

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Last Updated: Jun 27, 2025

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

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Published on: May 24, 2017

An Assay for Quantifying Protein-RNA Binding in Bacteria

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Published on: June 12, 2019

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Area of Science:

Biochemistry
Molecular Biology
Drug Discovery

Background:

Understanding small molecule-RNA interactions is crucial for developing RNA-targeted therapies.
Selectivity and binding properties are key challenges in designing RNA-binding molecules.

Purpose of the Study:

To develop and validate a novel system for large-scale analysis of small molecule-RNA interactions.
To profile the binding landscapes of specific small molecules and demonstrate the system's utility in discovering new RNA-binding agents.

Main Methods:

Utilized a multiplexed pull-down assay coupled with RNA structure libraries for high-throughput screening.
Employed G-clamp and thiazole orange derivatives to probe RNA structures and validate the assay.
Integrated fluorescent indicator displacement (FID) assays for screening RNA-binding molecules.

Main Results:

Successfully profiled the RNA-binding landscapes of G-clamp and thiazole orange derivatives.
Identified binding preferences of these molecules based on large-scale affinity profiles.
Demonstrated reliable screening results using high- and intermediate-rank RNAs in FID assays.

Conclusions:

The developed system provides fundamental insights into small molecule-RNA interactions.
This platform facilitates the efficient discovery of novel RNA-binding molecules for therapeutic applications.
The study highlights the importance of RNA structure libraries in understanding molecular recognition.