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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.
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Topoisomerases are divided into two main types. Type I...

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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...

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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...

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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...

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DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...

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Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

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Related Experiment Video

Updated: May 18, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Dynamics of DNA supercoils.

M T J van Loenhout¹, M V de Grunt, C Dekker

¹Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Lorentzweg 1, 2628CJ Delft, Netherlands.

Science (New York, N.Y.)

|September 18, 2012

Summary

Scientists directly visualized DNA plectonemes, revealing their dynamics and a novel fast hopping mechanism. This discovery explains how genome conformation rapidly reorganizes on a millisecond timescale.

Area of Science:

Molecular Biology
Biophysics
Genomics

Background:

DNA exists in a supercoiled state, featuring intertwined loops called plectonemes, which are crucial for cellular functions.
The dynamic behavior of DNA supercoiling and plectonemes is not well understood, limiting insights into genome regulation.

Purpose of the Study:

To directly visualize and characterize the dynamics of individual DNA plectonemes.
To investigate the factors influencing plectoneme formation and movement.
To identify novel mechanisms of plectoneme translocation along DNA.

Main Methods:

Direct visualization of individual plectoneme dynamics using advanced microscopy techniques.
Controlled manipulation of DNA stretching force and ionic strength to study their effects on plectonemes.

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Related Experiment Videos

Last Updated: May 18, 2026

Studying DNA Looping by Single-Molecule FRET

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Published on: June 28, 2014

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

High-speed imaging to capture rapid plectoneme translocation events.

Main Results:

Observed that the number of plectonemes is dependent on applied stretching force and ionic strength.
Demonstrated that plectonemes move via diffusion and an unexpected fast hopping mechanism.
Documented rapid (<20 milliseconds) long-range plectoneme displacement facilitated by nucleation at distant sites.

Conclusions:

Plectoneme dynamics are directly visualized, revealing key factors influencing their behavior.
A novel fast hopping mechanism enables rapid, long-distance genome reorganization.
This provides a new understanding of genome conformation dynamics on millisecond timescales.