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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...

Facilitated Transport

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...

Facilitated Transport

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...

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...

Facilitated Diffusion

Facilitated Diffusion

The plasma membrane, a critical structure in cellular biology, houses an array of transporters, or carrier proteins, interspersed within its lipid bilayer. These proteins play a crucial role in solute transport through facilitated diffusion, a form of passive diffusion that uses transporters to move the molecules across the membrane.
In this process, substrates such as organic compounds and ions interact with a transporter on one side, triggering conformational changes in proteins that enable...

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...

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Related Experiment Video

Updated: Jun 23, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

Facilitated diffusion with DNA coiling.

Michael A Lomholt¹, Bram van den Broek, Svenja-Marei J Kalisch

¹Department of Physics and Chemistry, MEMPHYS Center for Biomembrane Physics, University of Southern Denmark, Odense M, Denmark.

Proceedings of the National Academy of Sciences of the United States of America

|May 8, 2009

Summary

DNA-binding proteins use facilitated diffusion, alternating between 1D scanning and 3D searches. DNA coiling enables intersegmental jumps, enhancing target location efficiency, as shown by our theoretical model.

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A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

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

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Published on: March 1, 2022

Area of Science:

Molecular Biology
Biophysics
Computational Biology

Background:

DNA-binding proteins locate targets via facilitated diffusion, involving 1D sliding and 3D diffusion.
DNA coiling can lead to intersegmental jumps, where proteins rebind to distant DNA segments in 3D space.

Purpose of the Study:

To develop a theoretical model incorporating DNA coiling and intersegmental jumping.
To extend the facilitated diffusion model to account for DNA looping effects.

Main Methods:

Theoretical modeling of DNA-binding protein search dynamics.
Inclusion of spatial correlations of short hops and DNA coiling effects.
Quantitative analysis of intersegmental jumping at varying DNA densities.

Main Results:

The facilitated diffusion model was extended to include intersegmental jumping.
The model quantitatively explains the enhancement of target location by DNA-binding proteins.
DNA coiling significantly impacts protein search efficiency through intersegmental jumps.

Conclusions:

Intersegmental jumping is a crucial mechanism for DNA-binding proteins.
The theoretical approach provides a quantitative framework for understanding protein-DNA interactions.
This work elucidates how DNA structure influences protein search dynamics.