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

Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

2.9K
Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
2.9K
RNA Stability01:53

RNA Stability

36.2K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
36.2K
Improving Translational Accuracy02:07

Improving Translational Accuracy

15.4K
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...
15.4K

You might also read

Related Articles

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

Sort by
Same author

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026
Same author

LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.

Bioinformatics (Oxford, England)·2026
Same author

Proximity of the Histone-Acetylation Site to the Termini Shapes Phase Behavior with DNA.

Journal of the American Chemical Society·2026
Same author

Identification of ANT2 as a Druggable Target for Endocrine-Resistant ERα-Positive Breast Cancer.

International journal of molecular sciences·2026
Same author

Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.

Briefings in bioinformatics·2026
Same author

Caffeic acid suppresses cyclin D1 expression by directly binding to ribosomal protein S5 in colorectal cancer cells.

Scientific reports·2026

Related Experiment Video

Updated: Mar 28, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

5.4K

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

Shun Sakuraba1, Kiyoshi Asai1,2, Tomoshi Kameda2

  • 1Graduate School of Frontier Sciences, The University of Tokyo , 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan.

The Journal of Physical Chemistry Letters
|January 2, 2016
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations accurately predict RNA-RNA duplex stability. This study validates computational methods for estimating thermodynamic properties of RNA complexes, crucial for understanding structural stability.

Keywords:
Gibbs free energyHamiltonian replica exchange methodfree-energy perturbationnucleic acid

More Related Videos

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

8.8K
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

2.6K

Related Experiment Videos

Last Updated: Mar 28, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

5.4K
Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
09:15

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

Published on: November 21, 2017

8.8K
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

2.6K

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Biology

Background:

  • RNA-RNA duplexes are key structural components in biological systems.
  • Dimerization free energy quantifies the stability of RNA complexes.
  • Accurate estimation of thermodynamic properties is essential for predicting RNA behavior.

Purpose of the Study:

  • To comparatively analyze RNA-RNA duplex dimerization free-energy changes using molecular dynamics (MD) simulations and experimental data.
  • To validate the accuracy of MD simulations in estimating thermodynamic properties of RNA molecules.
  • To assess the capability of current molecular force fields in predicting RNA structural stability.

Main Methods:

  • Utilized molecular dynamics simulations to estimate dimerization free-energy changes for RNA-RNA duplexes.
  • Performed experimental measurements for comparison with simulation data.
  • Employed linear regression analysis to compare simulation results with experimental data for nine double-stranded RNA sequences (six base pairs each).

Main Results:

  • Achieved quantitative agreement between MD simulations and experimental data.
  • Linear regression yielded a mean absolute deviation of 0.55 kcal/mol and an R(2) value of 0.97.
  • Demonstrated the capability of MD simulations with current force fields to accurately estimate RNA thermodynamic properties.

Conclusions:

  • Molecular dynamics simulations provide a reliable method for estimating RNA-RNA duplex dimerization free energies.
  • The study validates the use of computational approaches for predicting the structural stability of RNA complexes.
  • Current molecular force fields are sufficiently accurate for assessing the thermodynamic properties of RNA molecules.