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

14.0K
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...
14.0K
DNA Topoisomerases02:02

DNA Topoisomerases

31.1K
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. ...
31.1K
DNA Helicases00:55

DNA Helicases

21.3K
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...
21.3K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
The Replisome03:01

The Replisome

33.3K
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
33.3K

You might also read

Related Articles

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

Sort by
Same author

A Ruthenium-BODIPY Photosensitizer for Light-Triggered Apoptosis in Triple-Negative Breast Cancer Cells.

Inorganic chemistry·2026
Same author

Excited-State Proton Transfer Dynamics in Betaine-Based Deep Eutectic Solvents: Is the Reaction Controlled by Solvent Relaxation?

The journal of physical chemistry. B·2026
Same author

Spectral Graph Entropy of Chromatin: A von Neumann Framework for Multiscale Polymer Organization from Hi-C.

The journal of physical chemistry. B·2026
Same author

An experimentally-informed polymer model reveals high resolution organization of genomic loci.

Nature communications·2026
Same author

Shape-Aware Diffusivity of DNA Binding Proteins Undergoing Rotation-Coupled Sliding Dynamics along DNA.

The journal of physical chemistry. B·2025
Same author

A dual-functional AIE luminogen for sensitive nitro explosive detection and efficient photolabeling.

Analytical methods : advancing methods and applications·2025

Related Experiment Video

Updated: Jun 16, 2025

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

3.1K

Nick Induced Dynamics in Supercoiled DNA Facilitates the Protein Target Search Process.

Sangeeta1, Arnab Bhattacherjee1

  • 1School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

The Journal of Physical Chemistry. B
|August 15, 2024
PubMed
Summary

DNA nicks release supercoiled DNA stress through writhing and twisting motions, increasing linking number. This enhances protein search dynamics, speeding up transcription by facilitating DNA-protein communication.

More Related Videos

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

6.7K
High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements
08:50

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements

Published on: May 12, 2023

2.0K

Related Experiment Videos

Last Updated: Jun 16, 2025

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

3.1K
CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

6.7K
High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements
08:50

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements

Published on: May 12, 2023

2.0K

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Supercoiled DNA accumulates torsional stress, impacting transcriptional machinery.
  • DNA nicks are known to alleviate this stress, but their precise role in protein dynamics is unclear.

Purpose of the Study:

  • To elucidate the molecular mechanisms by which DNA nicks release stress.
  • To investigate the impact of nicks on protein search dynamics crucial for transcription initiation and elongation.

Main Methods:

  • Extensive computer simulations were employed to model DNA nicking and its effects.
  • Analysis focused on DNA writhing, twisting, linking number changes, and torsional dynamics.

Main Results:

  • DNA nicks release intramolecular stress via writhing and twisting, leading to a step-like increase in linking number.
  • Nicked supercoiled DNA exhibits enhanced torsional dynamics and faster conformational changes.
  • Protein diffusion on nicked DNA is accelerated due to improved DNA-protein communication via juxtaposition site dynamics.

Conclusions:

  • DNA nicks are crucial for efficient transcription elongation by actively managing torsional stress during RNA polymerase unwinding.
  • The study reveals the mechanistic intricacies of how DNA nicks facilitate protein search and DNA unwinding.