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

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
The DNA Helix01:16

The DNA Helix

Overview
The DNA Helix01:07

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

You might also read

Related Articles

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

Sort by
Same author

hexABC seeking the physical code of DNA.

Nature communications·2026
Same author

Prognostic impact of pleural effusion in acute heart failure and its link to diuretic therapy.

The American journal of medicine·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

Efficient exploration of peptide libraries using active learning with AlphaFold-based screening.

bioRxiv : the preprint server for biology·2026
Same author

Beyond Classical Force Fields: Physics-Driven Assessment of the Grappa Machine-Learned Force Field on the FoldBind Dataset.

Chemphyschem : a European journal of chemical physics and physical chemistry·2026
Same author

Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains.

Journal of chemical information and modeling·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 18, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Exploring polymorphisms in B-DNA helical conformations.

Pablo D Dans1, Alberto Pérez, Ignacio Faustino

  • 1Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine, Parc Cientific de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.

Nucleic Acids Research
|September 27, 2012
PubMed
Summary
This summary is machine-generated.

The traditional model of DNA flexibility needs revision. New analysis reveals bimodal distributions in helical parameters, challenging the elastic nearest-neighbor model and suggesting a more complex reality for DNA mechanics.

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Related Experiment Videos

Last Updated: May 18, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • The conventional mesoscopic paradigm models DNA as elastic base-pair steps with harmonic oscillations.
  • Nearest-neighbor (NN) models simplify sequence effects, considering only 10 unique base-pair step cases.
  • Recent large-scale simulations indicate DNA flexibility is more complex than previously thought.

Purpose of the Study:

  • To challenge the elastic NN model of DNA flexibility.
  • To investigate the phenomenon of bimodal distributions in DNA helical parameters.
  • To propose improvements for mesoscopic DNA flexibility models.

Main Methods:

  • In-depth statistical analysis of extensive molecular dynamics (MD) trajectories.
  • Analysis of a large dataset of experimental DNA structures.
  • Identification and characterization of bimodal distributions in helical parameters.

Main Results:

  • Solid statistical evidence confirms the presence of bimodal distributions for certain DNA helical parameters.
  • These bimodal distributions represent a significant deviation from the predictions of the elastic NN model.
  • The findings highlight limitations in current mesoscopic models of DNA flexibility.

Conclusions:

  • The elastic NN model is insufficient to capture the full complexity of DNA flexibility.
  • Bimodality in helical parameters suggests DNA can adopt multiple stable conformations.
  • Improved mesoscopic models are needed to incorporate these deviations and provide a more accurate representation of DNA mechanics.