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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...

Fixing Double-strand Breaks

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...

Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...

Polytene Chromosomes

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...

Polytene Chromosomes

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jun 13, 2026

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Two distinct overstretched DNA states.

Hongxia Fu¹, Hu Chen, John F Marko

¹Research Centre of Excellence in Mechanobiology, 117543, Singapore.

Nucleic Acids Research

|May 4, 2010

Summary

This summary is machine-generated.

DNA overstretching involves two distinct pathways: strand unpeeling and a fast double-stranded elongation. Environmental factors like salt and temperature control which pathway dominates, revealing tunable DNA mechanics near physiological conditions.

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Last Updated: Jun 13, 2026

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Area of Science:

Biophysics
Molecular Biology
Biochemistry

Background:

The DNA double helix exhibits an 'overstretching' transition around 65 pN.
The precise mechanism of DNA overstretching, specifically strand separation, remains debated.

Purpose of the Study:

To elucidate the distinct mechanisms underlying DNA overstretching.
To investigate the influence of environmental factors on DNA overstretching pathways.

Main Methods:

Force-extension measurements of DNA.
Analysis of DNA overstretching transitions under varying conditions.

Main Results:

DNA overstretching involves two distinct processes: a slow, hysteretic 'unpeeling' and a fast, non-hysteretic elongation.
The relative proportion of these two states is sensitive to DNA sequence, salt concentration, and temperature.
A shift in the balance between unpeeling and elongation occurs under near-physiological conditions.

Conclusions:

DNA overstretching does not necessarily involve complete strand separation but can result in an elongated double-stranded state.
The physical properties of the DNA double helix are finely tuned, allowing environmental factors to selectively favor unpeeling or overextension.