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

RNA Structure01:19

RNA Structure

4.8K
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...
4.8K
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
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
6.1K
Nucleic Acids02:43

Nucleic Acids

44.1K
Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
44.1K
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
Types of RNA01:23

Types of RNA

63.6K
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
63.6K

You might also read

Related Articles

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

Sort by
Same author

Circumventing the Synthesizability Problem in Generative Molecular Design.

Journal of chemical information and modeling·2026
Same author

Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.

NAR genomics and bioinformatics·2026
Same author

Circumventing the synthesizability problem in generative molecular design.

bioRxiv : the preprint server for biology·2026
Same author

Neutrophil CD14 is a driver and a therapeutic target for deep vein thrombosis.

Blood advances·2026
Same author

Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.

Science advances·2026
Same author

RNA sequence design and protein-DNA specificity prediction with NA-MPNN.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Jun 28, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.5K

RNAscape: geometric mapping and customizable visualization of RNA structure.

Raktim Mitra1, Ari S Cohen1, Remo Rohs1,2,3,4

  • 1Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

Nucleic Acids Research
|April 17, 2024
PubMed
Summary

RNAscape visualizes RNA tertiary structures, preserving topology for mechanistic insights. This webserver offers intuitive, publication-quality images for RNA and DNA structures without coding.

More Related Videos

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

4.1K
Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

12.1K

Related Experiment Videos

Last Updated: Jun 28, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.5K
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

4.1K
Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

12.1K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Visualizing RNA's complex 3D structures and interactions is crucial for understanding molecular functions.
  • Existing secondary structure visualization tools often fail to preserve topological correspondence due to tertiary interactions.
  • Current tools do not account for quaternary interactions between multiple RNA molecules.

Purpose of the Study:

  • To develop a webserver, RNAscape, for generating topologically accurate and visually intuitive RNA structure visualizations.
  • To enable the analysis of RNA/DNA hybrid structures and DNA topologies, including G-quadruplexes.

Main Methods:

  • RNAscape employs a mathematical mapping algorithm prioritizing helical segments to maintain tertiary organization.
  • Non-helical segments are mapped to minimize visual clutter, ensuring clarity.
  • The webserver generates publication-quality images and supports non-standard nucleotides and various annotation styles.

Main Results:

  • RNAscape successfully produces visualizations that preserve topological correspondence.
  • The tool provides structurally insightful and visually intuitive representations of RNA molecules.
  • It supports user-uploaded 3D structures or Protein Data Bank (PDB) IDs and offers customization options.

Conclusions:

  • RNAscape is a valuable webserver for researchers needing to visualize and analyze complex RNA and DNA structures.
  • It overcomes limitations of previous tools by accurately representing tertiary and quaternary interactions.
  • The user-friendly interface requires no programming experience, making advanced structural analysis accessible.