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Related Concept Videos

DNA Topoisomerases02:02

DNA Topoisomerases

37.5K
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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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 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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The DNA Replication Fork01:02

The DNA Replication Fork

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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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The DNA Replication Fork01:02

The DNA Replication Fork

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Replication in Prokaryotes01:32

Replication in Prokaryotes

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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
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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Structural diversity of supercoiled DNA.

Rossitza N Irobalieva1,2, Jonathan M Fogg2,3,4, Daniel J Catanese2

  • 1Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030 USA.

Nature Communications
|October 13, 2015
PubMed
Summary

DNA supercoiling regulates genetic code access and DNA metabolism. This study reveals unique 3D structures and base exposure patterns in negatively and positively supercoiled DNA, offering new insights into DNA flexibility and function.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • DNA supercoiling is crucial for regulating DNA metabolism and genetic code accessibility.
  • Understanding the structural dynamics of supercoiled DNA, especially positively supercoiled forms, is essential but remains limited.

Purpose of the Study:

  • To investigate the three-dimensional conformations and structural behavior of individual DNA minicircle topoisomers with defined supercoiling degrees.
  • To elucidate how different supercoiling levels (negative and positive) influence DNA structure and base accessibility.

Main Methods:

  • Electron cryo-tomography was employed to visualize individual purified DNA minicircle topoisomers.
  • Biochemical analyses and molecular dynamics simulations were integrated to complement structural data.

Main Results:

  • Both negatively and positively supercoiled DNA topoisomers exhibit a wide distribution of unique three-dimensional conformations.
  • Increasing negative supercoiling leads to greater base exposure. Positively supercoiled DNA also shows exposed bases beyond a specific supercoiling threshold.
  • Molecular dynamics simulations confirm conformational heterogeneity and provide atomistic details on DNA flexibility.

Conclusions:

  • DNA supercoiling dictates distinct three-dimensional structures and conformational heterogeneity.
  • The study reveals differential base exposure mechanisms under varying torsional stress, crucial for DNA function.
  • This integrated approach provides essential structural insights into the functional dynamics of supercoiled DNA.