Related Experiment Video
Updated: Jun 19, 2026
10:59
Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
Published on: May 24, 2017
Ultrasonic cleavage of nicked DNA
I A Il'icheva1, D Yu Nechipurenko, S L Grokhovsky
1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, Russia. grok@imb.ac.ru.
Journal of Biomolecular Structure & Dynamics
|October 3, 2009
Summary
Ultrasound cleavage is significantly enhanced near nicks in double-stranded DNA (dsDNA), highlighting structural alterations over sequence-specific effects. This finding is crucial for understanding DNA repair mechanisms.
Area of Science:
- Biophysics
- Molecular Biology
- Structural Biology
Background:
- Nicked double-stranded DNA (dsDNA) plays a critical role in DNA repair processes.
- Understanding the structural properties of nicked dsDNA is essential for studying DNA integrity and repair pathways.
Purpose of the Study:
- To investigate the effect of ultrasound irradiation on nicked dsDNA fragments.
- To quantitatively assess ultrasonic cleavage rates in the vicinity of DNA nicks.
- To compare cleavage patterns in nicked vs. intact dsDNA.
Main Methods:
- Experimental study involving ultrasound irradiation of dsDNA fragments.
- Quantitative analysis of ultrasonic cleavage rates using polyacrylamide gel electrophoresis.
Main Results:
- Cleavage rates are significantly enhanced in regions approximately 10 base pairs (b.p.) up and down the nick.
- Ultrasonic cleavage intensity near the nick is an order of magnitude higher than in intact dsDNA.
- Cleavage rates decrease markedly beyond the nicked regions compared to intact dsDNA.
Conclusions:
- A nick in dsDNA represents a substantial structural alteration that overrides sequence-specific modulations.
- The nick acts as a focal point for enhanced ultrasonic cleavage, impacting DNA structural dynamics.
Related Concept Videos
01:08Nucleotide Excision Repair
Overview
01:38Nucleotide Excision Repair
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...
01:03Single-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...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
01:05Maxam-Gilbert Sequencing
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
02:04Fixing Double-strand Breaks
The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...