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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...

DNA Helicases

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...

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...

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...

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: Jun 22, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Internal dynamics of supercoiled DNA molecules.

Thomas Kalkbrenner¹, Axel Arnold, Sander J Tans

¹FOM Institute for Atomic and Molecular Physics (AMOLF), Kruislaan, Amsterdam, The Netherlands.

Biophysical Journal

|June 17, 2009

Summary

Supercoiled DNA shows faster internal motion, up to tenfold increase observed in submicrosecond dynamics. This accelerated diffusion in supercoiled DNA may stem from conformational constraints and altered persistence length.

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Area of Science:

Molecular Biology
Biophysics

Background:

Intramolecular diffusive motion in supercoiled DNA is crucial for gene regulation.
Previous studies indicated accelerated internal motion in intermediately supercoiled DNA.

Purpose of the Study:

To independently verify and characterize accelerated internal diffusive motion in fully supercoiled plasmid DNA.
To investigate the dynamics of supercoiled DNA using advanced fluorescent labeling and supercoiling techniques.

Main Methods:

Development of a method for fluorescently labeling a specific 200-bp region of DNA.
Efficient supercoiling of plasmid DNA using Escherichia coli gyrase.
Analysis of submicrosecond diffusive motion using fluorescence correlation spectroscopy.

Main Results:

Observed acceleration of intramolecular motion in fully supercoiled DNA by up to an order of magnitude compared to circular or linear DNA.
Identified an additional intermediate regime in the mean-square displacement over time, distinct from circular DNA.
Demonstrated faster submicrosecond dynamics within supercoiled DNA molecules.

Conclusions:

The study confirms accelerated internal diffusive motion in fully supercoiled DNA.
The observed dynamics suggest that conformational constraints and increased apparent persistence length contribute to the faster motion.
Further research is needed to fully elucidate the mechanisms behind this unexpected supercoiled DNA behavior.