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DNA Topoisomerases

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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: May 30, 2026

Analyzing Telomeric Protein-DNA Interactions Using Single-Molecule Magnetic Tweezers

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Force induced DNA melting.

Mogurampelly Santosh¹, Prabal K Maiti

¹Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore-12, India.

Journal of Physics. Condensed Matter : an Institute of Physics Journal

|August 6, 2011

Summary

Double-strand DNA overstretching and unzipping are force-induced melting transitions. Molecular dynamics simulations reveal DNA melting force decreases with temperature and differs based on pulling direction.

Area of Science:

Biophysics
Computational Biology
Molecular Biology

Background:

Double-strand DNA exhibits distinct mechanical behaviors under applied forces.
Understanding DNA's response to force is crucial for processes like replication and DNA-protein interactions.

Purpose of the Study:

To investigate DNA overstretching and unzipping transitions using atomistic molecular dynamics (MD) simulations.
To characterize these transitions as force-induced DNA melting phenomena.

Main Methods:

Fully atomistic molecular dynamics (MD) simulations.
Applying forces along and perpendicular to the DNA axis to induce overstretching and unzipping.
Analyzing conformational changes and base pair hydrogen bond breaking.

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Main Results:

DNA overstretching and unzipping are cooperative, force-induced melting transitions.
Melting force is dependent on pulling direction and decreases with increasing temperature.
Unzipping exhibits force-dependent jumps corresponding to base pair sequence variations.

Conclusions:

Both overstretching and unzipping can be viewed as forms of force-induced DNA melting.
The non-smooth melting behavior, particularly during unzipping, highlights the role of base pair sequence in DNA mechanics.