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

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

17.1K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
17.1K
Homologous Recombination02:31

Homologous Recombination

65.2K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
65.2K
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

16.0K
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
16.0K
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

4.6K
4.6K
DNA Topoisomerases02:02

DNA Topoisomerases

37.2K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
37.2K
DNA Helicases00:55

DNA Helicases

24.8K
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...
24.8K

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

Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity.

Nature communications·2026
Same author

Structural modeling reveals the mechanism of motor ATPase coordination during type IV pilus retraction.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.

bioRxiv : the preprint server for biology·2026
Same author

Visualizing poloidal orientation in DNA minicircles.

Biophysical journal·2026
Same author

DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.

Chemical science·2026

Related Experiment Video

Updated: Mar 21, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K

Transitions of Double-Stranded DNA Between the A- and B-Forms.

James T Waters1, Xiang-Jun Lu2, Rodrigo Galindo-Murillo3

  • 1School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.

The Journal of Physical Chemistry. B
|May 3, 2016
PubMed
Summary
This summary is machine-generated.

Double-stranded DNA (dsDNA) readily transitions from A-DNA to B-DNA in solution without an energy barrier. Sequence-dependent A-phobicity influences the speed of this DNA structural transition.

More Related Videos

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
05:32

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

1.9K
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

3.6K

Related Experiment Videos

Last Updated: Mar 21, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.4K
Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping
05:32

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

1.9K
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

3.6K

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Double-stranded DNA (dsDNA) exists in various conformations, notably B-DNA under physiological conditions and A-DNA under low water activity.
  • A-DNA can be locally induced in protein-DNA complexes, and B-DNA/A-DNA transitions are implicated in viral genome packaging.

Purpose of the Study:

  • To investigate the A-DNA to B-DNA transition dynamics in solution using molecular dynamics (MD) simulations.
  • To introduce and utilize the A-B Index (ABI) for quantifying DNA conformational changes along the A-B continuum.

Main Methods:

  • Analysis of existing B-DNA MD simulations and new MD simulations of the A-DNA to B-DNA transition.
  • Development and application of the A-B Index (ABI) to measure DNA conformation.
  • Characterization of the A/B junction in dsDNA using MD simulations.

Main Results:

  • The transition from A-DNA to B-DNA in solution at physiological ionic strength occurs rapidly (within 5 ns) with no observed energy barrier.
  • More A-phobic DNA sequences exhibit faster transition rates.
  • The A/B junction displays an average bend angle of 20-30° with fluctuations occurring on a ~10 ns timescale.

Conclusions:

  • dsDNA undergoes spontaneous and rapid transitions from A-DNA to B-DNA in solution.
  • Sequence-specific properties, like A-phobicity, significantly affect the kinetics of DNA conformational changes.
  • The A/B junction is a structurally characterized feature with dynamic bending properties relevant to DNA conformational flexibility.