Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

DNA Topoisomerases

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 Forks

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...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

The DNA Replication Fork

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...

Residual Stresses

Residual Stresses

Residual stresses reside in a structure even after removing the original stress inducer. This phenomenon often arises from varied plastic deformations across different parts of a structure. Consider a rod stretched beyond its yield point. It will not regain its original length due to permanent deformation. Even after load removal, the rod does not entirely lose stress because of uneven plastic deformations, resulting in residual stresses. The computation of these stresses in structures is...

DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

You might also read

Related Articles

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

Sort by

Same author

Why Do PETases Struggle with Crystalline PET? Catalytic Ensemble Sampling Reveals Molecular Bottlenecks.

The journal of physical chemistry letters·2026

Same author

Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.

Journal of chemical information and modeling·2026

Same author

pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.

bioRxiv : the preprint server for biology·2026

Same author

Making PLUMED Fly: A Tutorial on Optimizing Performance.

The journal of physical chemistry. B·2026

Same author

RNA Dynamics and Interactions Revealed Through Atomistic Simulations.

Annual review of physical chemistry·2026

Same author

Machine learning for RNA secondary structure prediction: a review of current methods and challenges.

RNA (New York, N.Y.)·2026

Search research articles

Related Experiment Video

Updated: May 25, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

RNA unwinding from reweighted pulling simulations.

Francesco Colizzi¹, Giovanni Bussi

¹SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy. colizzi@sissa.it

Journal of the American Chemical Society

|February 9, 2012

Summary

This study reveals the molecular dynamics of RNA base pair opening and closing, crucial for biological functions. Our findings provide a motion picture of helix opening, validated by experiments, and explain enzyme-driven unwinding.

More Related Videos

Magnetic Tweezers for the Measurement of Twist and Torque

Magnetic Tweezers for the Measurement of Twist and Torque

Published on: May 19, 2014

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

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

Published on: September 27, 2024

Related Experiment Videos

Last Updated: May 25, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Magnetic Tweezers for the Measurement of Twist and Torque

Magnetic Tweezers for the Measurement of Twist and Torque

Published on: May 19, 2014

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

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

Published on: September 27, 2024

Area of Science:

Molecular Biophysics
Computational Biology
RNA Biology

Background:

Forming and melting of RNA base pairs are essential conformational transitions for biological functions.
The dynamic steps of these RNA duplex transitions lack quantitative molecular-level characterization.

Purpose of the Study:

To quantitatively characterize the dynamic steps of RNA base pair opening and melting at the molecular level.
To provide a molecular motion picture of RNA helix opening.

Main Methods:

Atomistic pulling simulations were used to enforce the base opening process.
A novel reweighting scheme was developed to reconstruct free-energy profiles along reaction coordinates like solvation.
The approach was systematically applied to different base-pair combinations.

Main Results:

A detailed molecular motion picture of RNA helix opening was generated.
The free-energy profiles for base pair opening were reconstructed.
The results were validated against extensive experimental observations.
A link between RNA dynamics and enzyme-dependent unwinding mechanisms was established.

Conclusions:

The intrinsic dynamics of RNA duplexes have been elucidated.
These dynamics can rationalize the directionality observed in RNA-processing molecular machineries.
The study provides a molecular basis for understanding RNA conformational changes.