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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...

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...

The DNA Helix

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

The DNA Helix

The DNA Helix

The DNA Replication Fork

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...

The DNA Replication Fork

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork. Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...

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Related Experiment Video

Updated: May 13, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Dynamical simulations of DNA supercoiling and compression.

David Swigon¹, Sookkyung Lim, Yongsam Kim

¹Department of Mathematics, University of Pittsburgh, 511 Thackeray Hall, Pittsburgh, PA 15260, U.S.A. swigon@pitt.edu

Biochemical Society Transactions

|March 22, 2013

Summary

DNA dynamics and supercoiling were studied using a generalized immersed boundary method. Results show DNA collapses into compact configurations influenced by initial conditions and electric fields, deviating from thermodynamic equilibrium.

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Last Updated: May 13, 2026

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Area of Science:

Biophysics
Computational Biology
Molecular Dynamics

Background:

Understanding DNA dynamics is crucial for molecular biology.
DNA supercoiling is a fundamental process influenced by various factors.
Computational methods are essential for studying complex molecular behaviors.

Purpose of the Study:

To investigate the effects of electrostatic repulsion on DNA supercoiling dynamics.
To analyze DNA behavior in solution under a constant electric field.
To compare simulated DNA configurations with thermodynamic equilibrium predictions.

Main Methods:

Generalized immersed boundary method for DNA dynamics simulation.
Stochastic extension of the generalized immersed boundary method.
Analysis of DNA supercoiling, radius of gyration, and ellipticity ratio.

Main Results:

DNA supercoiling is sensitive to initial excess link and ionic strength.
Perturbed DNA collapses into compact supercoiled structures.
Electric fields compress DNA, reducing its radius of gyration and ellipticity ratio compared to equilibrium.

Conclusions:

Electrostatic repulsion significantly impacts DNA supercoiling.
DNA behavior in electric fields deviates from standard thermodynamic equilibrium.
The generalized immersed boundary method provides insights into DNA conformational changes.