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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...
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...
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...
Replication in Prokaryotes01:32

Replication in Prokaryotes

DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...

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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase
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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Published on: September 27, 2024

Exploring writhe in supercoiled minicircle DNA.

Jonathan M Fogg1, Natalia Kolmakova, Ian Rees

  • 1Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|September 28, 2011
PubMed
Summary
This summary is machine-generated.

Researchers generated supercoiled minicircle DNA using lambda-Int recombination. Divalent metal ions promote writhe in minicircles, revealing insights into DNA structure and electrostatic effects.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Structural Biology

Background:

  • Supercoiled DNA is crucial for cellular processes.
  • Minicircle DNA offers a simplified model for studying DNA supercoiling.
  • Understanding the partitioning of supercoiling into twist and writhe is essential.

Purpose of the Study:

  • To generate and characterize supercoiled minicircle DNA.
  • To investigate the influence of divalent metal ions on minicircle DNA conformation.
  • To elucidate the relationship between supercoiling, twist, writhe, and electrostatic effects.

Main Methods:

  • Lambda-Int recombination in E. coli for minicircle DNA production.
  • Purification of minicircles with defined superhelical density (ΔLk).
  • Gel electrophoresis and atomic force microscopy for structural analysis.

Main Results:

  • Milligram quantities of supercoiled minicircles were produced efficiently, down to 254 bp.
  • Purified 339 bp minicircles with unique ΔLk (0 to -6) were obtained.
  • Divalent cations (Ca2+, Mg2+) induced significant writhe in minicircles.
  • Electrostatic effects strongly influence DNA writhe in low ionic strength conditions.

Conclusions:

  • Minicircle DNA supercoiling can be partitioned into twist and writhe.
  • Divalent metal ions stabilize higher writhe conformations.
  • Electrostatic interactions play a critical role in DNA structural dynamics.
  • This study provides novel insights into minicircle DNA supercoiling and general DNA structure.