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

Proofreading01:31

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase Enzyme
Proofreading01:43

Proofreading

Synthesis of new DNA molecules starts when DNA polymerase links nucleotides together in a sequence that is complementary to the template DNA strand. DNA polymerase has a higher affinity for the correct base to ensure fidelity in DNA replication. The DNA polymerase furthermore proofreads during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.Errors during Replication Are Corrected by the DNA Polymerase EnzymeGenomic DNA is synthesized in...
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...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

You might also read

Related Articles

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

Sort by
Same author

A detailed molecular picture of protein folding during active translation.

bioRxiv : the preprint server for biology·2026
Same author

How proteins fold.

Nature reviews. Molecular cell biology·2026
Same author

Morphological and molecular evidence of the Antarctic sleeper shark <i>Somniosus antarcticus</i> (Somniosidae) in northern Chile.

PeerJ·2026
Same author

Single-Molecule methods to investigate mechanisms of transcription by RNA polymerase of Mycobacterium tuberculosis.

Methods (San Diego, Calif.)·2026
Same author

SmartTrap: automated precision experiments with optical tweezers.

Nature methods·2026
Same author

The Rossmann2×2 Fold Attains its Native Structure Via a Defined Pathway of Sequential and Cooperative Folding Units.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jun 21, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

Proofreading dynamics of a processive DNA polymerase.

Borja Ibarra1, Yann R Chemla, Sergey Plyasunov

  • 1Department of Physics, University of California, Berkeley, CA 94720-3220, USA.

The EMBO Journal
|August 8, 2009
PubMed
Summary

Investigating DNA primer transfer in Phi 29 DNA polymerase using single-molecule mechanics reveals novel intermediates. Mechanical tension mimics mismatched nucleotides, influencing primer repositioning during proofreading.

More Related Videos

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis
07:38

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

Published on: October 6, 2017

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

Related Experiment Videos

Last Updated: Jun 21, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis
07:38

DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis

Published on: October 6, 2017

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

Area of Science:

  • Molecular Biology
  • Biophysics
  • Enzymology

Background:

  • Replicative DNA polymerases possess intrinsic proofreading, involving DNA primer transfer between polymerization and exonuclease sites.
  • The precise dynamics of this primer transfer during active DNA synthesis are not fully understood.

Purpose of the Study:

  • To investigate the conformational dynamics of intramolecular DNA primer transfer during processive replication.
  • To explore the role of mechanical forces in this process for Phi 29 DNA polymerase and its mutants.

Main Methods:

  • Utilized a single-molecule mechanical assay to apply controlled tension to individual polymerase-DNA complexes.
  • Monitored conformational changes associated with DNA primer transfer during polymerase activity.

Main Results:

  • Mechanical tension was found to promote intramolecular primer transfer, similar to the effect of incorporating a mismatched nucleotide.
  • Two novel intermediates were identified: a tension-sensitive polymerization conformation and a non-active state potentially acting as a fidelity checkpoint.

Conclusions:

  • Single-molecule force spectroscopy can elucidate the dynamics of DNA primer transfer during polymerase proofreading.
  • The identified intermediates offer new insights into the fidelity mechanisms of replicative DNA polymerases.