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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...

Inhibitors of Bacterial DNA Synthesis

Inhibitors of Bacterial DNA Synthesis

Bacterial pathogens depend on precise and efficient DNA replication to sustain infection. Two type II topoisomerases—DNA gyrase and topoisomerase IV—are critical to this process, as they resolve DNA supercoiling and unlink chromosomes during replication. Fluoroquinolones, synthetic derivatives of quinolones, exploit this mechanism by stabilizing the transient DNA–enzyme cleavage complex, preventing strand religation, and causing lethal double-strand breaks. These antibiotics are selectively...

DNA Helicases

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...

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...

Nucleic Acid Structure

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

The Replisome

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

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Related Experiment Video

Updated: Jun 8, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Published on: November 1, 2012

Solution structures of DNA-bound gyrase.

Nicole M Baker¹, Steven Weigand, Sarah Maar-Mathias

¹Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.

Nucleic Acids Research

|September 28, 2010

Summary

Researchers revealed the structural arrangement of bacterial DNA gyrase complexes. This structural insight clarifies how DNA gyrase facilitates negative supercoiling, a crucial process for DNA replication and transcription.

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Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

DNA gyrase is essential for bacterial DNA replication and transcription.
The enzyme introduces negative supercoils into DNA through a complex mechanism involving ATP hydrolysis.
Understanding the structural basis of DNA gyrase function is key to developing novel antibiotics.

Purpose of the Study:

To elucidate the structural organization of bacterial DNA gyrase complexes during the initial stages of the supercoiling reaction.
To characterize the arrangement of DNA gyrase subunits and DNA fragments in the active complex.

Main Methods:

Sedimentation velocity experiments to determine complex size and shape.
Small-angle X-ray scattering (SAXS) to generate molecular envelopes of the gyrase/DNA complexes.
Characterization of complexes bound to 137- and 217-bp DNA fragments.

Main Results:

DNA gyrase formed elongated complexes with DNA fragments, exhibiting hydrodynamic radii of 70-80 Å.
SAXS data revealed 2-fold symmetric molecular envelopes.
The C-terminal domain (CTD) of the A subunit and the ATPase domain of the B subunit were located at opposite ends of the complexes.

Conclusions:

A structural model for DNA gyrase was proposed, with DNA binding along the sides and wrapping around the CTDs near the exit gate.
This model provides new insights into the mechanism of DNA negative supercoiling.
The findings contribute to a deeper understanding of DNA topology regulation in bacteria.