Related Experiment Video
Updated: Oct 23, 2025
12:29
Investigation of Protein Recruitment to DNA Lesions Using 405 Nm Laser Micro-irradiation
Published on: March 20, 2018
9.6K
TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation
J Ramos-Méndez1, J A LaVerne2, N Domínguez-Kondo3
1Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America.
Physics in Medicine and Biology
|August 19, 2021
Summary
The Geant4-DNA simulation code was updated to accurately model water radiolysis and DNA damage. New parameters improve predictions of chemical species yields and single-strand break induction by radiation.
Area of Science:
- Physics and Chemistry of Radiation Interactions
- Computational Biology and Biophysics
- Monte Carlo Simulations
Background:
- Accurate simulation of the chemical stage of water radiolysis is crucial for understanding radiation-induced DNA damage.
- Existing Geant4-DNA code required revisions to better align with experimental observations.
- Integration of detailed DNA geometry with chemical kinetics is essential for precise damage prediction.
Purpose of the Study:
- To revise and validate the chemical stage of the Geant4-DNA Monte Carlo simulation code.
- To improve the accuracy of predicting time-dependent yields of radiolytic species in water.
- To accurately simulate DNA damage, specifically single-strand breaks (SSB), induced by low linear energy transfer radiation.
Main Methods:
- Updated reaction rate coefficients and adjusted the root-mean-square (RMS) displacement parameter for water molecules in Geant4-DNA.
- Validated the revised code (Geant4-DNA/TOPAS-nBio) by comparing predicted time-dependent G-values and scavenger effects with experimental data for pure liquid water.
- Integrated DNA geometry with chemistry simulations to estimate SSB yields induced by 137Cs gamma-ray radiolysis of plasmid DNA.
Main Results:
- The revised Geant4-DNA/TOPAS-nBio showed improved agreement with experimental data for time-dependent G-values and scavenger effects.
- Simulated SSB induction efficiencies for hydroxyl radicals (•OH) and hydrogen radicals (H•) agreed well with non-homogeneous kinetic and step-by-step Monte Carlo models.
- An RMS displacement of 1.24 nm and specific SSB efficiencies (24% for •OH, 0.5% for H•) provided overall agreement with experimental uncertainties.
Conclusions:
- The enhanced Geant4-DNA/TOPAS-nBio code provides a fast, accurate, and user-friendly tool for simulating DNA damage.
- The simulation accurately predicts yields of radiolytic species and DNA damage under low LET irradiation.
- Further improvements in the spatial resolution of the DNA damage model may enhance agreement with direct experimental measurements.
More Related Videos
12:43Advanced Confocal Microscopy Techniques to Study Protein-protein Interactions and Kinetics at DNA Lesions
Published on: November 12, 2017
11.2K
09:39Author Spotlight: Combining Proximity Ligand Assay with Gamma-H2AX Staining to Characterize Protein Interactions in DNA Damage Response
Published on: August 2, 2024
669
Related Concept Videos
01:35Mutations
41.5K
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...
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
41.5K
01:38Nucleotide Excision Repair
4.1K
DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
4.1K
02:02DNA Topoisomerases
33.1K
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. ...
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
33.1K
02:37DNA Damage can Stall the Cell Cycle
9.6K
In response to DNA damage, cells can pause the cell cycle to assess and repair the breaks. However, the cell must check the DNA at certain critical stages during the cell cycle. If the cell cycle pauses before DNA replication, the cells will contain twice the amount of DNA. On the other hand, if cells arrest after DNA replication but before mitosis, they will contain four times the normal amount of DNA. With a host of specialized proteins at their disposal,cells must use the right protein at...
9.6K