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Related Concept Videos

RNA-seq03:21

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 microarray-based...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Updated: Jun 17, 2026

Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters
10:52

Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters

Published on: May 29, 2026

Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA

Siran Tian1, Tatjana Trcek2

  • 1Department of Biology, Johns Hopkins University.

Journal of Visualized Experiments : Jove
|June 15, 2026
PubMed
Summary
This summary is machine-generated.

Researchers developed a visual assay to detect and quantify intermolecular base pairing in RNA clusters. This method uses split Broccoli RNA reporters and fluorescence to assess RNA-RNA interactions in vitro.

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Visualization and Quantification of Intermolecular RNA Base Pairing in in vitro RNA Clusters Using Split Broccoli RNA Reporters
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Published on: December 2, 2009

Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA Biology

Background:

  • Multivalent intermolecular RNA-RNA interactions drive RNA clustering in vitro, independent of proteins.
  • Predictive methods like chemical probing and computational simulations exist, but direct assessment of base pairing in RNA clusters is limited.

Purpose of the Study:

  • To develop and present a novel visual assay for detecting and quantifying intermolecular base pairing within RNA clusters.
  • To enable the study of RNA-RNA interactions in protein-free in vitro systems.

Main Methods:

  • Utilized a split Broccoli RNA reporter system conjugated to fluorescently labeled RNAs.
  • Engineered complementary reporter sequences that dimerize to form the Broccoli RNA aptamer.
  • Employed DFHBI-1T, a fluorophore that emits green fluorescence upon binding to the dimerized aptamer.

Main Results:

  • The assay visually reports intermolecular base pairing through the appearance of green fluorescence upon RNA clustering.
  • Quantified base pairing by measuring DFHBI-1T fluorescence intensity.
  • Assessed the influence of in vitro RNA clustering conditions on intermolecular base pairing.

Conclusions:

  • The developed visual assay effectively detects and quantifies intermolecular base pairing in RNA clusters.
  • Provides a novel tool for studying RNA-RNA interactions in vitro.
  • Facilitates the understanding of how clustering conditions affect base pairing in RNA assemblies.