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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.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
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DNA as a Genetic Template02:05

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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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...
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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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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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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Studying DNA Looping by Single-Molecule FRET
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MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

Roberto Rossini1, Vipin Kumar2, Anthony Mathelier2

  • 1Department of Biosciences, University of Oslo, 0316, Oslo, Norway.

Genome Biology
|November 30, 2022
PubMed
Summary

We developed MoDLE, a fast computational tool for modeling DNA loop extrusion. This method accurately simulates genome-wide molecular contacts, advancing 3D genome structure research.

Keywords:
Hi-CLoop extrusionMicro-CStochastic modelingTAD

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • DNA loop extrusion is crucial for genome architecture and function.
  • Accurate modeling of 3D genome structure is essential for understanding biological processes.

Purpose of the Study:

  • Introduce MoDLE, a novel computational tool for modeling DNA loop extrusion.
  • Enable fast and accurate simulation of genome-wide molecular contacts.

Main Methods:

  • MoDLE employs fast, stochastic modeling of DNA loop extrusion.
  • Simulates realistic contact patterns genome-wide.
  • Optimized for efficiency on various computing platforms.

Main Results:

  • MoDLE achieves high accuracy in simulating contact maps, comparable to existing methods.
  • MoDLE is orders of magnitude faster than current approaches.
  • Enables rapid, large-scale simulations of 3D genome structure.

Conclusions:

  • MoDLE provides an efficient and accurate tool for modeling DNA loop extrusion.
  • Facilitates exploratory and predictive modeling of 3D genome organization.
  • Accelerates research in genomics and computational biology.