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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...
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...
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...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
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: Jun 29, 2026

Preparation of DNA-crosslinked Polyacrylamide Hydrogels
09:06

Preparation of DNA-crosslinked Polyacrylamide Hydrogels

Published on: August 27, 2014

Strain softening in stretched DNA.

Binquan Luan1, Aleksei Aksimentiev

  • 1Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, Illinois 61801, USA.

Physical Review Letters
|October 15, 2008
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations revealed DNA

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Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
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Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Related Experiment Videos

Last Updated: Jun 29, 2026

Preparation of DNA-crosslinked Polyacrylamide Hydrogels
09:06

Preparation of DNA-crosslinked Polyacrylamide Hydrogels

Published on: August 27, 2014

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
08:48

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Modeling

Background:

  • Understanding DNA mechanics is crucial for molecular biology.
  • DNA exhibits complex behavior under mechanical stress.

Purpose of the Study:

  • To characterize the microscopic mechanics of DNA stretching.
  • To investigate DNA behavior during overstretching transitions.

Main Methods:

  • Extensive molecular dynamics simulations were performed.
  • An anisotropic pressure-control method was employed.
  • A random-field Ising model was used for reconciliation.

Main Results:

  • Realistic force-extension dependences of DNA molecules were obtained.
  • A coexistence of B and S DNA domains was observed during overstretching.
  • Strain softening was observed in torsionally constrained DNA stretching.

Conclusions:

  • Simulations provide insights into DNA overstretching.
  • Observed phenomena align with experimental data.
  • The study enhances understanding of DNA structural transitions.