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

Proofreading01:43

Proofreading

59.5K
Overview
59.5K
Proofreading01:31

Proofreading

8.5K
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...
8.5K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

8.6K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.6K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

2.6K
2.6K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

3.0K
3.0K
Improving Translational Accuracy02:07

Improving Translational Accuracy

14.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
14.0K

You might also read

Related Articles

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

Sort by
Same author

Energetic gradients emerge in developing motor-microtubule structures.

bioRxiv : the preprint server for biology·2026
Same author

Evolution of error correction through a need for speed.

Science (New York, N.Y.)·2026
Same author

Motor-driven microtubule diffusion in a photobleached dynamical coordinate system.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

The Environment-Dependent Regulatory Landscape of the <i>E. coli</i> Genome.

bioRxiv : the preprint server for biology·2025
Same author

The Environment-Dependent Regulatory Landscape of the <i>E. coli</i> Genome.

ArXiv·2025
Same author

The proteome is a terminal electron acceptor.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same journal

The Role of Functional Groups in Substituted Benzoic Acids Used as Dopants in Liquid Crystal Mixtures on the Nematic-Isotropic Transitions.

The journal of physical chemistry. B·2026
Same journal

Hyperfine Coupling Quantifies Hole Delocalization in Triarylamine Radical Cations of D-χ-A Molecules.

The journal of physical chemistry. B·2026
Same journal

A Solvatochromic-Chemometric Framework to Resolve Subtle Polarity Microenvironment Differences in Cycloalkanes Driven by Molecular Conformation and Substituent Effects: A Proof-Of-Concept for Advanced Aviation Fuel Design.

The journal of physical chemistry. B·2026
Same journal

Selective Effects of Backbone Cyclization and Disulfide Bonding as Global Covalent Constraints on the Conformational Ensemble of Sunflower Trypsin Inhibitor-1.

The journal of physical chemistry. B·2026
Same journal

Europium Coordination Structure in Peptide Complexes Resolved with Simulation and X-ray Absorption Spectroscopy.

The journal of physical chemistry. B·2026
Same journal

Competitive Coordination and Structural Evolution of Phenylalanine-Mg<sup>2+</sup> Complexes in Microaqueous Environments: Insights from DFT and Molecular Dynamics Simulations.

The journal of physical chemistry. B·2026
See all related articles

Related Experiment Video

Updated: Jan 3, 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

10.1K

Allostery and Kinetic Proofreading.

Vahe Galstyan1, Rob Phillips2,3,4

  • 1Biochemistry and Molecular Biophysics Option , California Institute of Technology , Pasadena , California 91125 , United States.

The Journal of Physical Chemistry. B
|November 29, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a novel "piston model" for biological proofreading, replacing energy from hydrolysis with mechanical work. This model offers insights into optimizing speed, fidelity, and energy use in cellular error correction.

More Related Videos

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.6K
Eye-tracking to Distinguish Comprehension-based and Oculomotor-based Regressive Eye Movements During Reading
05:54

Eye-tracking to Distinguish Comprehension-based and Oculomotor-based Regressive Eye Movements During Reading

Published on: October 18, 2018

6.6K

Related Experiment Videos

Last Updated: Jan 3, 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

10.1K
Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

5.6K
Eye-tracking to Distinguish Comprehension-based and Oculomotor-based Regressive Eye Movements During Reading
05:54

Eye-tracking to Distinguish Comprehension-based and Oculomotor-based Regressive Eye Movements During Reading

Published on: October 18, 2018

6.6K

Area of Science:

  • Biophysics
  • Biochemistry
  • Molecular Biology

Background:

  • Kinetic proofreading is a crucial error correction mechanism in biological systems, typically relying on nucleotide hydrolysis for energy.
  • The precise management of energy consumption to enhance biological fidelity remains an area needing further investigation.

Purpose of the Study:

  • To introduce and explore the
  • piston model of proofreading
  • as an alternative to energy-dependent mechanisms.
  • To investigate how mechanical work can drive allosteric activation for enhanced proofreading fidelity.

Main Methods:

  • Conceptualizing a mechanical engine inspired by Feynman's ratchet and pawl mechanism to power piston actions.
  • Utilizing a mechanical design to systematically adjust parameters and analyze trade-offs between speed, fidelity, and energy dissipation.
  • Developing a theoretical framework for studying driven biochemical systems.

Main Results:

  • The piston model provides an intuitive explanation for optimal proofreading conditions.
  • Demonstrates that allosteric molecules can potentially exceed the Hopfield limit of fidelity by utilizing diverse states.
  • Highlights the role of mechanical work in driving enzyme activation and error correction.

Conclusions:

  • The piston model offers a new perspective on biological proofreading, decoupling it from direct reliance on nucleotide hydrolysis.
  • This framework facilitates the study of graded changes in speed, fidelity, and energy dissipation.
  • Suggests novel mechanisms for achieving high fidelity in biological processes through mechanical allosteric activation.