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 Structure01:23

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...
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...
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...
Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...

You might also read

Related Articles

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

Sort by
Same author

GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.

PLoS computational biology·2026
Same author

Automated Cephalometric Points Marking System.

Diagnostics (Basel, Switzerland)·2026
Same author

RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates.

Journal of molecular biology·2026
Same author

A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.

Nucleic acids research·2026
Same author

FRET-guided selection of RNA 3D structures.

Nucleic acids research·2026
Same author

RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces.

Journal of molecular biology·2025

Related Experiment Video

Updated: May 22, 2026

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

Automated 3D structure composition for large RNAs.

Mariusz Popenda1, Marta Szachniuk, Maciej Antczak

  • 1Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.

Nucleic Acids Research
|April 28, 2012
PubMed
Summary

A new automated method predicts RNA 3D structures from secondary structures using machine translation. This fast, high-quality RNA structure prediction tool, RNAComposer, aids in understanding RNA functions.

More Related Videos

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: May 22, 2026

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

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Determining the three-dimensional (3D) structure of Ribonucleic Acid (RNA) is crucial for understanding its diverse cellular functions.
  • Experimental methods for RNA structure determination face challenges, especially for large RNA molecules, creating a need for accurate computational prediction tools.

Purpose of the Study:

  • To introduce a novel, fully automated method for predicting the 3D structures of RNA molecules based on their secondary structure.
  • To provide a user-friendly platform for high-resolution RNA 3D structure prediction.

Main Methods:

  • The method employs a machine translation system, treating RNA structure prediction as a translation process from secondary to tertiary structure.
  • It utilizes the RNA FRABASE database, which contains a dictionary linking RNA secondary and tertiary structure elements.
  • The prediction algorithm is computationally efficient, generating initial 3D structures within seconds on a single processor.

Main Results:

  • The method successfully predicts high-quality 3D structures for large RNA molecules.
  • It does not require structural templates or RNA sequence alignment, enabling the prediction of previously unresolved native and artificial RNA structures.
  • The RNAComposer server offers interactive and batch modes for RNA structure modeling, supporting up to 500 residues.

Conclusions:

  • The developed method offers a fast and accurate approach for automated RNA 3D structure prediction.
  • RNAComposer facilitates the study of RNA structure-function relationships by making structure prediction more accessible.
  • This approach broadens the scope of RNA structure modeling to include molecules without existing structural data.