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Related Concept Videos

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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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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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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.
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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...
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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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Related Experiment Video

Updated: Jun 20, 2025

Author Spotlight: Unraveling the Dynamics of Eukaryotic DNA Replication Through Single-Molecule Visualization
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Author Spotlight: Unraveling the Dynamics of Eukaryotic DNA Replication Through Single-Molecule Visualization

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Large bubble drives circular DNA melting.

Souradeep Sengupta1, Somendra M Bhattacharjee1, Garima Mishra1

  • 1Department of Physics, Ashoka University, Sonipat, Haryana - 131029, India. garima.mishra@ashoka.edu.in.

Physical Chemistry Chemical Physics : PCCP
|July 19, 2024
PubMed
Summary
This summary is machine-generated.

Circular DNA melting is driven by large bubbles, similar to linear DNA. Smaller circular DNA exhibits higher thermal stability due to transient bubbles, an effect that decreases with increasing length.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • DNA melting is crucial for biological processes.
  • Supercoiling influences DNA stability and melting.
  • Understanding circular DNA melting is essential for various applications.

Purpose of the Study:

  • Investigate the melting transition of non-supercoiled circular DNA.
  • Compare melting behavior of circular and linear DNA.
  • Analyze the effect of DNA length on thermal stability.

Main Methods:

  • Brownian dynamics simulations.
  • Analysis of sector-wise changes in average base-pair distance.
  • Modeling of DNA melting transitions.

Main Results:

  • Melting of circular DNA is primarily driven by a large bubble formation.
  • Circular DNA melting behavior closely resembles that of linear DNA.
  • Shorter circular DNA shows increased thermal stability compared to linear DNA, attributed to transient small bubbles.

Conclusions:

  • Non-supercoiled circular DNA melting is characterized by large bubble formation.
  • Length-dependent thermal stability differences between circular and linear DNA exist at short scales.
  • Transient small bubbles contribute to the enhanced stability of smaller circular DNA.