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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. ...

Mutations

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

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Related Experiment Video

Updated: Dec 27, 2025

Author Spotlight: Combining Proximity Ligand Assay with Gamma-H2AX Staining to Characterize Protein Interactions in DNA Damage Response

Author Spotlight: Combining Proximity Ligand Assay with Gamma-H2AX Staining to Characterize Protein Interactions in DNA Damage Response

Published on: August 2, 2024

A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio.

Hongyu Zhu^1,2,3, Aimee L McNamara^1,4, Jose Ramos-Mendez⁵

¹Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America.

Physics in Medicine and Biology

|February 27, 2020

Summary

This summary is machine-generated.

Monte Carlo simulations predict DNA damage, but results vary widely due to parameter choices. This study quantifies how physics, chemistry models, and specific parameters significantly impact DNA double-strand break (DSB) predictions.

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Last Updated: Dec 27, 2025

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Area of Science:

Radiation biology
Computational biophysics
Radiobiology

Background:

Monte Carlo (MC) simulations are crucial for modeling radiation-induced DNA damage at the nanoscale.
Simulation outcomes are highly sensitive to chosen physics and chemistry parameters, leading to inter-study variability.

Purpose of the Study:

To investigate the impact of physics and chemistry models on DNA damage prediction using MC simulations.
To quantify the effect of key parameters on DNA double-strand break (DSB) induction.

Main Methods:

Utilized a detailed nuclear DNA model for geometry.
Employed the TOPAS-nBio MC toolkit to simulate radiation interactions.
Varied physics/chemistry models and parameters: direct damage energy threshold, chemical stage duration, and hydroxyl radical reaction probability.

Main Results:

Physics and chemistry models alone altered DSB yields by up to 34% and 16%, respectively.
Parameter variations showed significant impacts: direct damage threshold (28%), chemical stage length (51%), and hydroxyl radical probability (71%).

Conclusions:

Simulation parameter choices critically influence predicted DNA double-strand break yields.
Standardizing parameters and models is essential for reliable MC-based radiobiology research.