Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.5K
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...
3.5K
RNA-seq03:21

RNA-seq

9.9K
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...
9.9K
Experimental RNAi02:15

Experimental RNAi

6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Designing molecular RNA switches with Restricted Boltzmann machines.

Nature communications·2025
Same author

DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.

Nucleic acids research·2025
Same author

A Multiscale Study to Characterize SHAPE Probe/RNA Molecules Prereactive Complex and Its Role in Initiating the SHAPE Reaction.

Journal of chemical information and modeling·2025
Same author

Investigation of a squaramide motif as a bioisostere of the amino-acid group of S-adenosyl-L-methionine and its functional impact on RNA methylation.

Communications chemistry·2025
Same author

IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.

NAR genomics and bioinformatics·2025
Same author

Copper catalyzed cycloaddition for the synthesis of non isomerisable 2' and 3'-regioisomers of arg-tRNA<sup>arg</sup>.

Methods (San Diego, Calif.)·2024
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jun 12, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.0K

SHAPE Probing to Screen Computationally Designed RNA.

Pierre Hardouin1, Francois-Xavier Lyonnet du Moutier1, Bruno Sargueil2

  • 1CiTCOM, Cibles Thérapeutiques et Conception de Médicaments, UMR8038 CNRS, Université Paris Cité, Paris, France.

Methods in Molecular Biology (Clifton, N.J.)
|September 23, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces a streamlined workflow and software tools to rapidly screen thousands of designed RNA sequences. This accelerates RNA design for synthetic biology and RNA-based therapies by simplifying experimental analysis.

Keywords:
Chemical probingFootprintIPANEMAPRNA structure prediction

More Related Videos

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.4K
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

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

Published on: February 17, 2023

3.5K

Related Experiment Videos

Last Updated: Jun 12, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.0K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.4K
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

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

Published on: February 17, 2023

3.5K

Area of Science:

  • Synthetic Biology
  • RNA Therapeutics
  • Computational Biology

Background:

  • RNA design is crucial for synthetic biology and RNA-based therapies, but current methods rely on inefficient trial-and-error.
  • High-throughput RNA structure probing (e.g., SHAPE-MaP) enables rapid, large-scale analysis but generates complex data.
  • Analyzing numerous experimental results for subtle sequence differences is time-consuming and challenging.

Purpose of the Study:

  • To develop an integrated experimental and analytical workflow for efficient screening of numerous designed RNA sequences.
  • To simplify and expedite the analysis of high-throughput RNA structure probing data.
  • To provide a user-friendly software solution for RNA design and evaluation.

Main Methods:

  • Implementation of a novel experimental workflow for high-throughput RNA sequence screening.
  • Development of the 'shapemap tools' software suite for customized data analysis.
  • Integration of chemical probing data with computational analysis for sequence evaluation.

Main Results:

  • The proposed workflow successfully eases the screening of thousands of designed RNA sequences simultaneously.
  • The 'shapemap tools' software suite provides a customized solution for analyzing complex RNA structure probing data.
  • Significant reduction in the time and effort required for evaluating experimental results.

Conclusions:

  • The developed workflow and software tools accelerate RNA design pipelines.
  • This approach facilitates the advancement of synthetic biology and RNA-based therapeutic development.
  • The tools offer a scalable solution for analyzing large-scale RNA structure data.