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Related Concept Videos

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...
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...
Overview of DNA Repair02:25

Overview of DNA Repair

In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
Protein Denaturation01:28

Protein Denaturation

The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...
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...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...

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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Published on: September 27, 2024

Single DNA denaturation and bubble dynamics.

Ralf Metzler1, Tobias Ambjörnsson, Andreas Hanke

  • 1Physics Department, Technical University of Munich, James Franck Strasse, 85747 Garching, Germany.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|August 6, 2011
PubMed
Summary
This summary is machine-generated.

DNA denaturation bubbles can open spontaneously and proliferate with increasing temperature or force. This study uses the Poland-Scheraga model to analyze DNA bubble dynamics and proposes a new method to measure bubble coalescence.

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Related Experiment Videos

Last Updated: May 30, 2026

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
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Published on: September 27, 2024

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DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
08:00

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

Area of Science:

  • Biophysics
  • Molecular Biology
  • Thermodynamics

Background:

  • DNA typically exists as a stable double helix under physiological conditions.
  • Local denaturation bubbles can form spontaneously due to thermal fluctuations.
  • These bubbles can expand, leading to full DNA denaturation.

Purpose of the Study:

  • To investigate the equilibrium and dynamics of DNA denaturation bubbles using the Poland-Scheraga model.
  • To compare theoretical predictions with recent single-molecule DNA experiments.
  • To propose a novel single-molecule setup for studying bubble coalescence and DNA breathing dynamics.

Main Methods:

  • Application of the Poland-Scheraga model to analyze DNA denaturation.
  • Comparison of theoretical models with experimental data from single DNA chain experiments.
  • Design of a new single-molecule setup with dual bubble zones.

Main Results:

  • The study analyzes DNA denaturation transitions and bubble dynamics below, at, and above the denaturation point.
  • A new experimental setup is proposed to measure bubble coalescence.
  • The interplay between denaturation bubbles and single-stranded DNA binding proteins is considered.

Conclusions:

  • The Poland-Scheraga model provides a framework for understanding DNA denaturation bubble behavior.
  • The proposed experimental setup offers a novel approach to quantify DNA breathing parameters.
  • Understanding DNA bubble dynamics is crucial for studying DNA-protein interactions.