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

DNA Topoisomerases02:02

DNA Topoisomerases

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.  Type I...
Replication in Prokaryotes01:32

Replication in Prokaryotes

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...
Replication in Prokaryotes02:35

Replication in Prokaryotes

Overview
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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...
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...
Replication in Eukaryotes01:29

Replication in Eukaryotes

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
Many Proteins Orchestrate Replication at the Origin
Eukaryotic replication follows many of the same...

You might also read

Related Articles

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

Sort by
Same author

Reversal of tracer advection and Hall drift in an interacting chiral fluid.

Physical review. E·2026
Same author

Single-trajectory Bayesian modeling reveals multi-state diffusion of the MSH sliding clamp.

NPJ systems biology and applications·2026
Same author

Anomalous statistics in the Langevin equation with fluctuating diffusivity: from Brownian yet non-Gaussian diffusion to anomalous diffusion and ergodicity breaking.

Reports on progress in physics. Physical Society (Great Britain)·2026
Same author

Tau condensation on DNA mediates microtubule attachment suggesting a mitotic role for centromere-localized tau.

Nature communications·2026
Same author

Anomalous diffusion and fluctuations in complex systems and networks.

Chaos (Woodbury, N.Y.)·2026
Same author

Fractional Brownian motion with mean-density interaction: A myopic self-avoiding fractional stochastic process.

Physical review. E·2025
Same journal

Erratum: Spectroscopy and Ground-State Transfer of Ultracold Bosonic ^{39}K^{133}Cs Molecules [Phys. Rev. Lett. 135, 203401 (2025)].

Physical review letters·2026
Same journal

Erratum: Lifetime of the ^{2}F_{7/2} Level in Yb^{+} for Spontaneous Emission of Electric Octupole Radiation [Phys. Rev. Lett. 127, 213001 (2021)].

Physical review letters·2026
Same journal

Laser-Plasma Based Seeded Free Electron Laser in the High-Gain Regime.

Physical review letters·2026
Same journal

Parent Hamiltonians for Stabilizer Quantum Many-Body Scars.

Physical review letters·2026
Same journal

Properties of Heavy Cosmic Nuclei Phosphorus, Chlorine, Argon, Potassium, and Calcium: Results from the Alpha Magnetic Spectrometer.

Physical review letters·2026
Same journal

Role of Spin-Isospin Symmetries in Nuclear β-Decays.

Physical review letters·2026
See all related articles

Related Experiment Video

Updated: Jun 5, 2026

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks
12:19

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

Published on: November 10, 2016

Supercoiling induces denaturation bubbles in circular DNA.

Jae-Hyung Jeon1, Jozef Adamcik, Giovanni Dietler

  • 1Department of Physics, Technical University of Munich, 85747 Garching, Germany.

Physical Review Letters
|January 15, 2011
PubMed
Summary
This summary is machine-generated.

Supercoiling can cause DNA denaturation bubbles, especially in AT-rich regions. Experiments confirm these DNA bubbles exist in free solution, impacting DNA structure.

More Related Videos

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Related Experiment Videos

Last Updated: Jun 5, 2026

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks
12:19

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

Published on: November 10, 2016

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Area of Science:

  • Biophysics
  • Molecular Biology
  • Genetics

Background:

  • DNA supercoiling is a critical factor influencing DNA structure and function.
  • Denaturation bubbles, or open regions, can form in double-stranded DNA under certain conditions.
  • Understanding these phenomena is key to comprehending DNA replication, transcription, and packaging.

Purpose of the Study:

  • To develop a theoretical framework for the thermodynamic properties of supercoiling-induced denaturation bubbles in circular DNA.
  • To investigate the influence of DNA supercoiling, salt concentration, and sequence on bubble formation.
  • To provide an analytical derivation for the probability of multiple bubble occurrences.

Main Methods:

  • Theoretical modeling of DNA supercoiling and denaturation thermodynamics.
  • Analytical derivation of probability distributions for bubble formation.
  • Experimental validation using single DNA plasmid imaging in free solution.

Main Results:

  • DNA supercoiling, salt concentration, and sequence heterogeneity significantly impact bubble occurrence.
  • A probability distribution for multiple bubbles in supercoiled DNA was derived.
  • Experimental evidence confirmed the existence of DNA bubbles in free solution.
  • Sustained in vivo DNA bubbles are likely due to twist release in AT-rich regions.

Conclusions:

  • The theoretical framework accurately describes supercoiling-induced DNA denaturation bubbles.
  • Experimental results validate the theoretical predictions.
  • The findings highlight the biological relevance of DNA bubbles in processes like replication and transcription.