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DNA Topoisomerases

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 Proteins

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 Packaging

DNA Packaging

DNA Packaging

DNA Packaging

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

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Related Experiment Video

Updated: May 23, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Anharmonic stacking in supercoiled DNA.

¹School of Science and Technology-CNISM, University of Camerino, Camerino, Italy. marco.zoli@unicam.it

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

|April 13, 2012

Summary

This summary is machine-generated.

DNA denaturation is stabilized by stacking anharmonicity, which strengthens hydrogen bonds. Twisting is crucial for understanding DNA

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Related Experiment Videos

Last Updated: May 23, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Area of Science:

Biophysics
Computational Biology
Molecular Dynamics

Background:

DNA denaturation involves the separation of double strands.
Understanding thermal stability is key to DNA function.

Purpose of the Study:

Analyze multistep denaturation in short circular DNA.
Investigate the role of helicoidal geometry and nonlinear effects.

Main Methods:

Mesoscopic Hamiltonian model
Path integral method for computing melting profiles

Main Results:

Stacking anharmonicity stabilizes DNA against thermal disruption.
Twisting is essential for capturing nonlinear thermodynamic properties.
Moderately untwisted DNA helices are more stable than overtwisted ones.

Conclusions:

Nonlinear effects, particularly twisting and stacking anharmonicity, significantly influence DNA stability.
Untwisted DNA conformations better resist strand separation.