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 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...
The Replisome03:01

The Replisome

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 the...
The Replisome03:01

The Replisome

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 the...
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...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
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...

You might also read

Related Articles

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

Sort by
Same author

Effect of ensemble averaging on Green-Kubo estimation of short-time stress relaxation modulus in all-atom molecular dynamics simulations of an unentangled polymer melt.

The Journal of chemical physics·2026
Same author

Accelerated Combinatorial Drug Design for Human Immunodeficiency Virus Resistance through Seeded Multisite λ-Dynamics.

Journal of chemical theory and computation·2026
Same author

Correction to "Identifying Artifacts from Large Library Docking".

Journal of medicinal chemistry·2025
Same author

Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.

Journal of chemical theory and computation·2025
Same author

Autobiography of Charles L. Brooks III.

The journal of physical chemistry. B·2025
Same author

Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics.

Journal of chemical information and modeling·2025

Related Experiment Video

Updated: Jun 13, 2026

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG
10:11

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG

Published on: July 26, 2024

Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling.

Kenji Yoshimoto1, Karunesh Arora, Charles L Brooks

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.

Biophysical Journal
|April 23, 2010
PubMed
Summary

Simian Virus 40 helicase moves along DNA through sequential ATP binding, not concerted binding. DNA interactions and ATP pocket opening guide this unidirectional motor protein motion.

More Related Videos

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
07:37

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Published on: September 27, 2024

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
08:28

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

Related Experiment Videos

Last Updated: Jun 13, 2026

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG
10:11

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG

Published on: July 26, 2024

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
07:37

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Published on: September 27, 2024

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
08:28

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Hexameric helicases are ATP-dependent motor proteins crucial for nucleic acid processing.
  • Understanding their translocation mechanisms is key to comprehending DNA replication and repair.

Purpose of the Study:

  • To investigate the dynamic behavior of Simian Virus 40 (SV40) helicase during DNA translocation.
  • To elucidate the molecular features governing the helicase's unidirectional motion.

Main Methods:

  • Utilized coarse-grained molecular dynamics simulations.
  • Analyzed the interactions between the helicase, DNA, and ATP binding events.

Main Results:

  • Attractive DNA-binding domain interactions are essential for unidirectional helicase motion.
  • Sequential ATP binding, not concerted binding, drives directional translocation.
  • The order of sequential ATP binding dictates the direction of helicase movement.
  • ATP binding in one pocket induces asymmetric pocket opening, coordinating sequential binding.

Conclusions:

  • Helicase function relies on sequential ATP binding, with directionality controlled by binding order.
  • Asymmetric pocket deformation is a key mechanism for coordinating directional motor protein activity.
  • Findings offer insights into substrate translocation mechanisms in other motor proteins.