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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...
Restarting Stalled Replication Forks02:37

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 Recombination02:31

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 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...
Replication in Prokaryotes01:32

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 18, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Macroscopic loop formation in circular DNA denaturation.

Alkan Kabakçıoğlu1, Amir Bar, David Mukamel

  • 1Department of Physics, Koç University, Sarıyer 34450 İstanbul, Turkey.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 26, 2012
PubMed
Summary
This summary is machine-generated.

Statistical mechanics reveal DNA denaturation differs under fixed linking number. A macroscopic loop forms in the overtwisting scenario, similar to supercoiling, with its size dependent on temperature.

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Last Updated: May 18, 2026

Studying DNA Looping by Single-Molecule FRET
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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Area of Science:

  • Statistical mechanics
  • Biophysics
  • DNA structure and dynamics

Background:

  • DNA denaturation under fixed linking number presents unique statistical mechanics compared to unconstrained DNA.
  • Two models exist for denatured loop formation: expense of overtwist or supercoils.
  • Supercoiling mechanism resembles Bose-Einstein condensation, with a macroscopic loop appearing at a critical temperature (Tc).

Purpose of the Study:

  • To investigate the nature of the denatured phase in the overtwisting scenario of DNA denaturation.
  • To determine if a macroscopic loop also appears in the overtwisting model.
  • To calculate the size of this macroscopic loop as a function of temperature.

Main Methods:

  • Extending earlier theoretical results on DNA denaturation.
  • Applying principles of statistical mechanics to model DNA overtwisting.
  • Calculating the size of denatured loops and their fraction relative to total loops.

Main Results:

  • A macroscopic loop appears in the overtwisting scenario, analogous to the supercoiling case.
  • The size of this macroscopic loop is calculated as a function of temperature.
  • The fraction of microscopic loops decreases above the critical temperature (Tc), exhibiting a cusp at Tc.

Conclusions:

  • The overtwisting mechanism of DNA denaturation also leads to the formation of a macroscopic loop.
  • This finding unifies the understanding of DNA denaturation under fixed linking number, regardless of whether overtwist or supercoils are involved.
  • The temperature dependence of the macroscopic loop size and the behavior of microscopic loops provide critical insights into DNA phase transitions.