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Related Concept Videos

DNA Topoisomerases02:02

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 Proteins01:03

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...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
The DNA Replication Fork01:02

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...
DNA as a Genetic Template02:05

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...
DNA Helicases00:55

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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Related Experiment Video

Updated: May 15, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

The interplay between supercoiling and DNA modifying enzymes at the single-molecule level.

Elise M Wilkinson1, Antoine M van Oijen1, Timothy D Craggs2

  • 1Molecular Horizons and School of Science, University of Wollongong, Wollongong, NSW, Australia.

Scientific Reports
|May 13, 2026
PubMed
Summary

DNA supercoiling, the twisting of DNA, affects enzyme activity. Studies show supercoiling enhances restriction enzyme cleavage efficiency, revealing DNA topology

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Last Updated: May 15, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

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Published on: June 28, 2014

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
05:58

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Published on: September 6, 2024

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
09:52

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

Published on: January 31, 2019

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • DNA supercoiling is crucial for DNA processes but often ignored in relaxed DNA studies.
  • Plectonemes are supercoiled structures formed by DNA overwinding or underwinding.
  • Understanding supercoiling's role is vital for comprehending DNA-enzyme interactions.

Purpose of the Study:

  • To investigate the effect of DNA supercoiling on enzyme activity at the single-molecule level.
  • To visualize and analyze DNA supercoiling dynamics and plectoneme formation.
  • To determine how DNA topology influences restriction enzyme function.

Main Methods:

  • Construction of topologically constrained 18-kb linear DNA substrates.
  • Induction of positive and negative supercoiling using intercalating dyes.
  • Single-molecule observation using Total Internal Reflection Fluorescence (TIRF) microscopy.
  • Assessing the activity of the restriction enzyme EcoRV on supercoiled DNA.

Main Results:

  • Direct visualization of plectonemes diffusing on DNA.
  • Plectonemes were observed to be stationary at EcoRV binding sites.
  • EcoRV exhibited increased cleavage efficiency on supercoiled DNA, with unaffected binding.
  • Supercoiling was found to enhance the kinetic interplay between DNA topology and enzyme activity.

Conclusions:

  • DNA supercoiling significantly modulates the activity of DNA modifying enzymes like EcoRV.
  • Supercoiling may make DNA cleavage more energetically favorable for enzymes that bend DNA.
  • This study highlights the importance of DNA topology in regulating enzymatic processes.