Related Experiment Video
Updated: Jun 26, 2026

06:51
Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
Published on: May 6, 2020
Multinuclear non-heme iron complexes for double-strand DNA cleavage
Rik P Megens1, Tieme A van den Berg, A Dowine de Bruijn
1Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Chemistry (Weinheim an Der Bergstrasse, Germany)
|January 9, 2009
Summary
Multinuclear iron complexes, unlike single-iron mimics, effectively cleave double-strand DNA. Trinuclear iron complexes are the most potent agents, likely due to simultaneous delivery of oxidizing equivalents for DNA damage.
Area of Science:
- Bioinorganic Chemistry
- Medicinal Chemistry
- Molecular Biology
Background:
- Bleomycin (BLM) anti-tumor drug activity is linked to its iron complex (Fe-BLM) inducing oxidative DNA damage.
- Mononuclear iron complexes like Fe-N4Py model Fe-BLM but only achieve single-strand DNA cleavage.
- Double-strand DNA cleavage requires two oxidizing equivalents, suggesting multinuclear complexes may be more effective.
Purpose of the Study:
- To synthesize and evaluate multinuclear iron complexes for enhanced oxidative double-strand DNA cleavage.
- To investigate the structure-activity relationship of ditopic and tritopic iron complexes in DNA cleavage.
- To compare the efficacy of multinuclear complexes against mononuclear models.
Main Methods:
- Synthesis of ditopic and tritopic N4Py-derived ligands.
- Formation and characterization of corresponding mononuclear, dinuclear, and trinuclear iron complexes.
- Evaluation of DNA cleavage activity using supercoiled pUC18 plasmid DNA assays.
Main Results:
- Dinuclear iron complexes exhibited significantly enhanced double-strand DNA cleavage compared to mononuclear Fe-N4Py.
- The structure of the linking moiety in dinuclear complexes did not substantially affect cleavage activity.
- Covalent attachment of a 9-aminoacridine intercalator did not improve double-strand DNA cleavage.
- Trinuclear iron complexes demonstrated the highest efficiency in oxidative double-strand DNA cleavage.
Conclusions:
- Multinuclear iron complexes, particularly trinuclear ones, are superior agents for oxidative double-strand DNA cleavage.
- The enhanced activity of trinuclear complexes is attributed to the increased probability of simultaneous delivery of two oxidizing equivalents to DNA.
- These findings offer a promising strategy for developing more effective DNA-cleaving agents for therapeutic applications.
More Related Videos
Related Concept Videos
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...
Fixing 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...
Fixing 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...
Homologous 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...
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...
Types and Mechanism of action
Topoisomerases are divided into two main types. Type I...
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...

