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

35.8K
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. ...
35.8K
Receptor-mediated Endocytosis01:38

Receptor-mediated Endocytosis

111.4K
Overview
111.4K
Antibody Structure01:10

Antibody Structure

65.7K
Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
65.7K
Molecules and Compounds02:38

Molecules and Compounds

69.4K
Atoms and Molecules
69.4K
DNA Helicases00:55

DNA Helicases

24.2K
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...
24.2K
The DNA Helix01:16

The DNA Helix

157.9K
Overview
157.9K

You might also read

Related Articles

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

Sort by
Same author

Genome-wide association study of paediatric bacteraemia and sepsis.

EBioMedicine·2026
Same author

Direct Counting of mRNA Copies Inside Individual Lipid Nanoparticles Using In Situ Lysis and Labeling.

Analytical chemistry·2026
Same author

Human genetic ancestry, <i>Mycobacterium tuberculosis</i> diversity, and tuberculosis disease severity in Dar es Salaam, Tanzania.

eLife·2026
Same author

New frontiers in applied biophysics: advancing drug discovery using single-molecule microscopy.

Biophysical reviews·2026
Same author

TORCphysics: a physical model of DNA-topology-controlled gene expression.

Nucleic acids research·2026
Same author

An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences.

NAR genomics and bioinformatics·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: Feb 11, 2026

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified &#955; DNA at the Single Molecule Level
08:56

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified λ DNA at the Single Molecule Level

Published on: July 17, 2018

8.0K

Visualizing structure-mediated interactions in supercoiled DNA molecules.

Shane Scott1, Zhi Ming Xu1, Fedor Kouzine2

  • 1Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada.

Nucleic Acids Research
|April 24, 2018
PubMed
Summary
This summary is machine-generated.

Directly visualizing DNA topology, this study reveals how supercoiling and temperature affect probe binding to unwinding sites. Increased negative supercoiling and temperature enhance DNA probe binding rates.

More Related Videos

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

1.3K
Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking
16:21

Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking

Published on: March 10, 2014

18.3K

Related Experiment Videos

Last Updated: Feb 11, 2026

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified &#955; DNA at the Single Molecule Level
08:56

Visualizing the Interaction Between the Qdot-labeled Protein and Site-specifically Modified λ DNA at the Single Molecule Level

Published on: July 17, 2018

8.0K
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

1.3K
Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking
16:21

Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking

Published on: March 10, 2014

18.3K

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • DNA topology, including supercoiling, significantly influences DNA structure and function.
  • Understanding DNA-protein and DNA-ligand interactions is crucial for molecular biology.
  • Existing methods for studying DNA binding kinetics can introduce artifacts.

Purpose of the Study:

  • To directly visualize and quantify topology-mediated interactions between DNA and probe molecules.
  • To investigate the influence of DNA supercoiling and temperature on binding kinetics.
  • To assess how DNA secondary structures modulate binding site accessibility.

Main Methods:

  • Utilized Convex Lens-induced Confinement (CLiC) imaging to trap DNA within nanopits.
  • Employed fluorescent probes to monitor binding to specific DNA unwinding sites on supercoiled plasmids.
  • Measured DNA-probe exchange rates and binding kinetics in situ.
  • Performed numerical simulations to model site-unwinding probabilities.

Main Results:

  • Demonstrated that plasmid structure, including secondary structures, affects probe binding.
  • Observed an increased binding rate of fluorescent probes with rising temperature and negative supercoiling.
  • Found that temperature dependence of binding kinetics can differentiate effects of competing DNA structures like Z-DNA.

Conclusions:

  • CLiC provides artifact-free measurements of DNA-ligand binding kinetics.
  • DNA supercoiling and temperature are critical factors regulating the accessibility of unwinding sites.
  • This approach enables the study of higher-order DNA structures' impact on local DNA conformation and binding events.