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 Structure01:23

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-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...
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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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 has a double-helix structure. The...

You might also read

Related Articles

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

Sort by
Same author

Design and discovery of 'tug-of-war' riboswitches.

bioRxiv : the preprint server for biology·2026
Same author

High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.

Nucleic acids research·2026
Same author

In Vitro Detection of Glyphosate by Coupling Enzymatic Conversion and Transcriptional Biosensors.

ACS synthetic biology·2026
Same author

De novo design of RNA pseudoknots with deep learning.

bioRxiv : the preprint server for biology·2026
Same author

Cell-free biosensors: where have we been and where do we need to go?

Current opinion in biotechnology·2026
Same author

Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.

bioRxiv : the preprint server for biology·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: May 18, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

An RNA Mapping DataBase for curating RNA structure mapping experiments.

Pablo Cordero1, Julius B Lucks, Rhiju Das

  • 1Department of Biochemistry and Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA.

Bioinformatics (Oxford, England)
|September 15, 2012
PubMed
Summary
This summary is machine-generated.

Researchers created the RNA Mapping Database (RMDB) for comparing RNA structure mapping experiments. This database aids in understanding RNA sequence, structure, and mapping data relationships.

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

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

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Related Experiment Videos

Last Updated: May 18, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

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

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • High-throughput sequencing, accelerated software, and large-scale mutagenesis have increased RNA structure mapping data.
  • A need exists for a curated database with error estimates and tools for data sharing, visualization, search, and meta-analysis.
  • The RNA Mapping Database (RMDB) addresses this need by centralizing and organizing RNA structure mapping data.

Purpose of the Study:

  • To establish a comprehensive database for RNA structure mapping experiments.
  • To facilitate comparisons of structural, thermodynamic, and kinetic properties of RNA.
  • To provide tools for exploring, analyzing, and hypothesizing RNA secondary structures.

Main Methods:

  • Development of an online front-end for the RMDB.
  • Implementation of data visualization tools including heat-maps, bar-graphs, and colored secondary structure graphics.
  • Standardization of data download formats (RDAT, SNRNASM) for computational analysis.

Main Results:

  • The RMDB currently houses 53 entries, encompassing over 2848 experiments for 1098 RNA constructs.
  • Data covers various solution conditions and is rapidly expanding.
  • The database enables users to generate secondary structure hypotheses from mapping data.

Conclusions:

  • The RMDB provides a valuable resource for researchers studying RNA structure and function.
  • It enables cross-experiment comparisons and hypothesis generation for RNA sequence/structure relationships.
  • The database is a growing, centralized repository for single-nucleotide-resolution RNA structure mapping data.