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 Stability01:53

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 Stability01:53

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...
DNA Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...

You might also read

Related Articles

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

Sort by
Same author

Viral RNAs as Dual Graphs: Extending the Motif Universe of RNAs.

bioRxiv : the preprint server for biology·2026
Same author

Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.

Biophysical journal·2026
Same author

VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels.

ArXiv·2026
Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026
Same author

Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism of <i>Xist</i>.

bioRxiv : the preprint server for biology·2026
Same author

Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.

The journal of physical chemistry. B·2026
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 29, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Predicting coaxial helical stacking in RNA junctions.

Christian Laing1, Dongrong Wen, Jason T L Wang

  • 1Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA.

Nucleic Acids Research
|September 16, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a computational method using random forests to predict RNA junction structures and topologies. The approach accurately identifies coaxial stacking and classifies junction types, aiding in RNA 3D structure prediction.

Related Experiment Videos

Last Updated: May 29, 2026

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 bioinformatics
  • RNA structure analysis

Background:

  • RNA tertiary structures involve complex arrangements of helices.
  • Understanding RNA junctions is crucial for predicting 3D RNA structures.
  • Accurate prediction of junction topology and coaxial stacking is needed.

Purpose of the Study:

  • To develop a computational method for predicting coaxial helical stacking and junction topology at the secondary structure level.
  • To classify junction topologies in RNA molecules.
  • To improve the accuracy of RNA 3D structure prediction through better junction analysis.

Main Methods:

  • Utilized a data mining approach, specifically random forests, employing decision trees.
  • Trained models using junction length, sequence, and other relevant variables.
  • Developed a web server, Junction-Explorer, for practical application.

Main Results:

  • Achieved 81% accuracy in predicting coaxial stacking for three-way junctions and 77% for four-way junctions.
  • Accuracy increased to 83% and 87% respectively when incorporating junction family type.
  • Predicted junction family with 85% accuracy for three-way and 74% for four-way junctions.

Conclusions:

  • The random forest-based method effectively predicts coaxial stacking and junction topology in RNA.
  • The developed tool, Junction-Explorer, aids in understanding RNA structural configurations.
  • Further improvements are needed for predicting junctions with more than four ways due to limited training data.