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...
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...
Nucleic Acids02:43

Nucleic Acids

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, the...
Nucleic acids02:43

Nucleic acids

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, the...

You might also read

Related Articles

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

Sort by
Same author

Transition Mechanism of the Human Dopamine Transporter via Molecular Dynamics Simulations.

Journal of chemical information and modeling·2026
Same author

Surgical treatment of giant diagonal branch aneurysms accompanied by obstructive coronary artery disease with guidance from 3D printed models: a case report.

BMC cardiovascular disorders·2026
Same author

Integrated Clinical and Proteomic Profiling of CD19 Chimeric Antigen Receptor T Cell Therapy in Progressive Systemic Sclerosis.

Arthritis & rheumatology (Hoboken, N.J.)·2026
Same author

Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform.

ACS sensors·2026
Same author

A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution.

bioRxiv : the preprint server for biology·2026
Same author

MGAPep: LLM-Augmented Multimodal Graph Attention for Protein-Peptide Binding Site Prediction and Cross-Domain Transfer.

IEEE journal of biomedical and health informatics·2026

Related Experiment Video

Updated: Jun 8, 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

Coarse-grained model for simulation of RNA three-dimensional structures.

Zhen Xia1, David Paul Gardner, Robin R Gutell

  • 1Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712, USA.

The Journal of Physical Chemistry. B
|October 2, 2010
PubMed
Summary

This study introduces a coarse-grained potential to predict RNA 3D structures from primary sequences. The method accurately models small RNA molecules, aiding experimental design and understanding RNA functions.

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

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

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Related Experiment Videos

Last Updated: Jun 8, 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

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

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

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Accurate RNA 3D structure prediction is crucial for understanding RNA function and guiding experiments.
  • Current methods may be computationally intensive or lack accuracy for diverse RNA structures.

Purpose of the Study:

  • To develop and validate a general coarse-grained (CG) potential for predicting RNA 3D structures.
  • To assess the performance of the CG potential in molecular dynamics simulations and folding studies.

Main Methods:

  • Developed a CG potential representing each nucleotide with five pseudoatoms for backbone and base interactions.
  • Parametrized the potential using statistical analysis of 688 experimental RNA structures.
  • Performed molecular dynamics simulations and simulated annealing on 15 RNA molecules (12-27 nucleotides).

Main Results:

  • CG potential simulations showed performance comparable to all-atom simulations.
  • Simulated annealing successfully generated native-like structures for ~75% of tested systems.
  • Accurate 3D structure prediction within 6.5 Å of native structures was achieved for all 15 RNAs using limited secondary structure information.

Conclusions:

  • The developed CG potential reliably predicts 3D structures for small RNA molecules when combined with limited secondary structure information.
  • This approach offers a computationally efficient alternative for RNA structure modeling.
  • Further exploration included using an all-atom force field to refine CG simulation outputs.