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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...

Single-Strand DNA Binding Proteins

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...

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...

Coordination of Gene Expression Processes in Bacteria

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...

The Replisome

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...

Replication in Prokaryotes

Replication in Prokaryotes

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...

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Related Experiment Video

Updated: May 17, 2026

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

Published on: November 10, 2016

Actively Induced Supercoiling Can Slow Down Plasmid Solutions by Trapping the Threading Entanglements.

Roman Staňo^1,2, Renáta Rusková^3,4, Dušan Račko³

¹Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.

|May 15, 2026

Summary

Supercoiling agents rapidly induce topological changes in ring polymers, forming stable clusters. This nonequilibrium process controls polymer dynamics, creating novel vitrified materials.

Keywords:

DNA active matter glass gyrase ring polymer supercoiling topology

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Last Updated: May 17, 2026

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

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Published on: November 10, 2016

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Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

Published on: August 21, 2016

Area of Science:

Soft matter physics
Polymer science
Materials science

Background:

Ring polymer topology influences material properties.
Supercoiled DNA plasmids resist relaxation by forming helical structures.
In equilibrium, supercoiled rings relax faster than relaxed rings due to threading.

Purpose of the Study:

To investigate the nonequilibrium dynamics of ring polymers under induced supercoiling.
To explore how supercoiling agents alter polymer topology and dynamics.
To demonstrate the potential for creating activity-vitrified materials.

Main Methods:

Molecular simulations were employed.
A supercoiling agent was simulated to induce rapid supercoiling in relaxed plasmids.
The conformational changes and relaxation dynamics of ring polymers were analyzed.

Main Results:

Supercoiling agents transformed ring polymer topology from open to branched.
Threaded rings were locked into slowly relaxing supramolecular clusters.
Nonequilibrium conditions were shown to significantly alter polymer dynamics.

Conclusions:

Polymer topology under nonequilibrium conditions can be harnessed to tune dynamic behavior.
Activity-induced clustering offers a route to create novel materials.
This work suggests a method for creating driven materials vitrified by activity.