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Related Concept Videos

DNA Topoisomerases02:02

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...
DNA Helicases00:55

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...
Single-Strand DNA Binding Proteins01:03

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...
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
Fixing Double-strand Breaks02:04

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...

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Related Experiment Video

Updated: Jun 26, 2026

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks
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Published on: November 10, 2016

Supercoil-accelerated DNA threading intercalation.

Pär Nordell1, Erik T Jansson, Per Lincoln

  • 1Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden. par.nordell@chalmers.se

Biochemistry
|January 24, 2009
PubMed
Summary
This summary is machine-generated.

DNA supercoiling significantly enhances threading rates for a ruthenium complex into plasmid DNA. However, high supercoiling can hinder further binding, impacting gene expression efficiency.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Chemical Biology

Background:

  • DNA supercoiling is a critical factor influencing DNA structure and function.
  • Understanding DNA-protein interactions is essential for gene regulation and drug development.

Purpose of the Study:

  • To investigate the impact of DNA supercoiling on the threading intercalation of a dimeric ruthenium complex.
  • To explore the relationship between DNA torsional strain, threading kinetics, and gene expression.

Main Methods:

  • Plasmid DNA (supercoiled and linear) was used as a substrate.
  • Kinetics of dimeric ruthenium complex threading were measured.
  • Luciferase gene expression was monitored to assess functional impact.

Main Results:

  • Threading rate into negatively supercoiled DNA was 2 orders of magnitude higher than into linear DNA at low binding density.
  • Further saturation was kinetically hampered in supercoiled DNA compared to relaxed DNA.
  • Threading kinetics correlated with inhibition of luciferase expression.

Conclusions:

  • DNA torsional strain can be leveraged to control DNA threading kinetics.
  • This control mechanism influences gene expression efficiency.
  • Ruthenium complexes show potential for modulating DNA-based processes.