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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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Mechanical Protein Functions01:58

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Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force. 
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DNA Helicases00:55

DNA Helicases

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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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Nucleosome Remodeling02:54

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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Lagging Strand Synthesis01:59

Lagging Strand Synthesis

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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
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The Replisome03:01

The Replisome

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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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Author Spotlight: Investigating the Motion Dynamics of the Eukaryotic Replisome Components at the Single-Molecule Level
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Structural Dynamics and Mechanochemical Coupling in DNA Gyrase.

Aakash Basu1, Angelica C Parente2, Zev Bryant3

  • 1Department of Physics, University of Illinois at Urbana-Champaign,Urbana, IL 61801, USA.

Journal of Molecular Biology
|March 27, 2016
PubMed
Summary

DNA gyrase is a molecular motor that uses ATP to supercoil DNA. Recent biophysical studies reveal its complex mechanics and coordination with DNA processes like transcription.

Keywords:
FRETmagnetic tweezersmolecular motorsingle-moleculetopoisomerase

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Gyrase functions as a molecular motor, utilizing ATP hydrolysis to perform mechanical work on DNA.
  • The enzyme introduces negative supercoiling, requiring coordination of DNA cleavage, religation, and conformational changes.

Purpose of the Study:

  • To present a current understanding of mechanochemical coupling in DNA gyrase.
  • To highlight diverse biophysical approaches revealing molecular architectures and conformational dynamics.

Main Methods:

  • Diverse biophysical approaches
  • Single-molecule assays

Main Results:

  • Detailed molecular architectures and new conformational intermediates were revealed.
  • Structural transitions modulated by ATP binding and the influence of mechanics on motor function were elucidated.
  • Reciprocal relationships between DNA supercoiling and transcription were illuminated.

Conclusions:

  • Mechanochemical coupling in DNA gyrase is complex, involving coordinated protein and DNA dynamics.
  • Understanding gyrase mechanics provides insights into chromosomal biology and interactions with other molecular machines.