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Related Concept Videos

DNA Topoisomerases02:02

DNA Topoisomerases

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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.
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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...
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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...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Homologous Recombination02:31

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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...
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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DNA-Topology Simplification by Topoisomerases.

Andreas Hanke1, Riccardo Ziraldo2, Stephen D Levene2,3,4

  • 1Department of Physics and Astronomy, University of Texas Rio Grande Valley, 1 W University Blvd, Brownsville, TX 78520, USA.

Molecules (Basel, Switzerland)
|July 2, 2021
PubMed
Summary
This summary is machine-generated.

DNA topology, including supercoiling and knotting, is vital for cellular processes. This study introduces a non-equilibrium network approach to better understand how enzymes called topoisomerases manage DNA topology.

Keywords:
DNA topologymaster equationsnon-equilibrium biophysicssite-specific recombinationtype-II topoisomerases

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • DNA topological properties like supercoiling, knotting, and catenation are crucial for fundamental biological processes including gene expression, replication, and chromosome segregation.
  • Non-trivial DNA topologies can impede molecular machinery but also facilitate DNA-sequence recognition through structural distortions.
  • Topoisomerases are essential enzymes that regulate DNA topology by passing DNA strands, with some utilizing ATP and others acting independently.

Purpose of the Study:

  • To investigate the management of DNA topology by topoisomerases.
  • To explore the non-equilibrium behavior of type-II topoisomerases, particularly their topology simplification activity.
  • To apply a novel non-equilibrium topological-network approach to study DNA topology dynamics.

Main Methods:

  • Utilized a non-equilibrium topological-network approach, diverging from conventional equilibrium models.
  • Focused on analyzing the rates of individual transitions between different topological states of DNA.
  • Employed circular DNA as a model system to assay supercoil formation/relaxation and knot/catenane resolution.

Main Results:

  • The study provides insights into the rates governing transitions between DNA topological states.
  • The non-equilibrium approach offers a new perspective on the detailed behavior of type-II topoisomerases.
  • Quantitative analysis of individual transition rates was achieved.

Conclusions:

  • The developed quantitative approach offers a new framework for studying topoisomerase activity.
  • This non-equilibrium perspective is expected to advance both experimental and computational modeling of topoisomerases.
  • Understanding DNA topology management is key to comprehending essential cellular functions.