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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

You might also read

Related Articles

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

Sort by
Same author

Nucleation of NaCl crystals from solution: Rate prediction and influence of noisy order parameters on the committor.

The Journal of chemical physics·2026
Same author

Combining multiple interface set path ensembles with MBAR reweighting.

The Journal of chemical physics·2026
Same author

TAV2b Peptide Derivatives Underwind and Stabilize Double-Stranded RNA upon Binding.

Journal of the American Chemical Society·2026
Same author

A Self-Organized Liquid Reaction Container for Cellular Memory.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Activation of colloidal patchy particle networks.

Soft matter·2025
Same author

Optimal kinetics for catalytic cycles from a single path-sampling simulation.

Proceedings of the National Academy of Sciences of the United States of America·2025
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: Jun 3, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

MDNA : a software module for DNA structure generation and analysis.

Thor van Heesch1, Enrico Skoruppa2, Peter G Bolhuis1

  • 1Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands.

Nucleic Acids Research
|June 2, 2026
PubMed
Summary
This summary is machine-generated.

MDNA is a new molecular modeling toolkit for creating complex DNA structures and modifications. It aids in generating accurate starting configurations for molecular simulations and analyzing DNA dynamics.

More Related Videos

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

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

Related Experiment Videos

Last Updated: Jun 3, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

Area of Science:

  • Molecular Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Understanding DNA's dynamical and structural properties is crucial for biological processes.
  • Existing tools struggle with complex DNA assemblies and modifications, limiting accurate simulation setups.

Purpose of the Study:

  • Introduce MDNA, a molecular modeling toolkit to overcome limitations in DNA structure generation and analysis.
  • Enable the creation of intricate DNA configurations with biologically relevant modifications for advanced simulations.

Main Methods:

  • Utilize a spline-based mapping technique for generating DNA shapes with arbitrary configurations.
  • Incorporate support for non-canonical base modifications (e.g., Hoogsteen transitions, DNA methylation).
  • Employ Monte Carlo minimization for structure refinement and rigid body formalism for geometric analysis.

Main Results:

  • MDNA enables the construction and detailed analysis of complex DNA structures.
  • The toolkit supports diverse DNA modifications and accurate geometric evaluation.
  • Integration of structure generation and analysis in a Python interface streamlines workflows.

Conclusions:

  • MDNA facilitates the modeling of complex DNA configurations, including modifications.
  • The toolkit enhances the study of DNA dynamics and DNA-protein interactions.
  • MDNA supports accurate starting configurations for molecular simulation studies.