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

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 Structure

RNA Structure

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

RNA Stability

RNA Stability

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...

You might also read

Related Articles

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

Sort by

Same author

Viscoelasticity analysis of coarse-grained cytoskeletal simulations with Cytosim and Cytocalc.

Biophysical journal·2026

Same author

Giant multicellular magnetotactic prokaryotes in marine sediments.

The ISME journal·2026

Same author

Patterns of active dipolar particles in external magnetic fields.

Physical review. E·2026

Same author

A magnetotactic bacterium capable of magnetic sensing.

iScience·2025

Same author

Geometry effects on protein mobility in a synapse.

Biophysical journal·2025

Same author

Enhanced condensate fluidity in modified patchy particle models.

The Journal of chemical physics·2025

Search research articles

Related Experiment Video

Updated: May 4, 2026

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

Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models.

Michael Faber¹, Stefan Klumpp¹

¹Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|December 17, 2013

Summary

This study introduces a new structure-based method to simulate RNA folding dynamics. The method accurately predicts RNA folding rates, aligning well with experimental data for various structures.

More Related Videos

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Related Experiment Videos

Last Updated: May 4, 2026

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

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

Biochemistry
Computational Biology
Molecular Biophysics

Background:

RNA molecules fold into complex 3D structures essential for their function.
Understanding RNA folding dynamics is crucial for predicting biochemical activity.

Purpose of the Study:

To introduce a novel structure-based computational method for studying RNA secondary structure folding dynamics.
To validate the method's accuracy in predicting folding rates against experimental data.

Main Methods:

Utilizing a structure-based approach focusing on native contacts.
Employing empirical free energies for parametrization.
Performing Kinetic Monte Carlo simulations for RNA folding, including free folding and folding under external force.

Main Results:

Simulations showed good agreement with experimental data for simple hairpins and complex structures like tRNA.
A strong correlation was observed between simulated and experimental folding rates.
The method demonstrates the ability to predict folding rates within approximately one order of magnitude.

Conclusions:

The developed structure-based method is a reliable tool for studying RNA folding dynamics.
This approach provides a valuable means for predicting RNA folding rates with reasonable accuracy.
The findings contribute to a deeper understanding of RNA structure-function relationships.