Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA Structure

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 Structure

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 Structure

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 Structure

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...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

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

Sort by

Same author

Multi-ancestry GWAS analysis identifies two novel loci associated with diabetic eye disease and highlights APOL1 as a high risk locus in patients with diabetic macular edema.

PLoS genetics·2023

Same author

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype.

Cell reports. Medicine·2023

Same author

A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk.

Scientific reports·2022

Same author

Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration.

Proceedings of the National Academy of Sciences of the United States of America·2018

Same author

Enabling genome-wide association testing with multiple diseases and no healthy controls.

Gene·2018

Same author

Analysis of protein-altering variants in telomerase genes and their association with MUC5B common variant status in patients with idiopathic pulmonary fibrosis: a candidate gene sequencing study.

The Lancet. Respiratory medicine·2018

Same journal

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.

Current protocols in bioinformatics·2020

Same journal

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

Current protocols in bioinformatics·2020

Same journal

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Current protocols in bioinformatics·2020

Same journal

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Current protocols in bioinformatics·2020

Same journal

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics·2020

Same journal

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Current protocols in bioinformatics·2020

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 22, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNA secondary structure analysis using the RNAshapes package.

Jens Reeder¹, Robert Giegerich²

¹University of Colorado, Boulder, Colorado.

Current Protocols in Bioinformatics

|June 5, 2009

Summary

This summary is machine-generated.

The RNAshapes package predicts RNA secondary structures using minimum free energy or weighted ensemble methods. It also offers a protocol for predicting consensus structures from related RNA sequences.

More Related Videos

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

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Related Experiment Videos

Last Updated: Jun 22, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Predicting RNA secondary structure is crucial for understanding RNA function.
Existing methods have limitations in accuracy and scope.

Purpose of the Study:

To demonstrate the utility of the RNAshapes package for RNA secondary structure prediction.
To provide a protocol for both single-sequence and consensus structure prediction.

Main Methods:

Utilizing the RNAshapes package for secondary structure prediction.
Employing minimum free energy (MFE) calculations.
Applying weighted ensemble (WE) simulations.
Implementing a protocol for consensus structure prediction across multiple related sequences.

Main Results:

Successful prediction of RNA secondary structures for individual sequences.
Accurate consensus structure prediction for sets of related RNA sequences.
Demonstration of RNAshapes package's versatility and ease of use.

Conclusions:

The RNAshapes package is a powerful tool for RNA secondary structure prediction.
The provided protocols facilitate efficient and accurate structure analysis.
This work aids researchers in exploring RNA structure-function relationships.