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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
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Fixing Double-strand Breaks02:04

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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Single-Strand DNA Binding Proteins01:03

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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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The DNA Replication Fork01:02

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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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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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Updated: Nov 14, 2025

Fabrication of Three-Dimensional Graphene-Based Polyhedrons via Origami-Like Self-Folding
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Defect-Induced Double-Stranded DNA Unwinding on Graphene.

Da Gao1, Baoyu Li2, Yanmei Yang3

  • 1School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.

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|March 10, 2021
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Defective graphene (D-Gra) unwinds double-stranded DNA (dsDNA) more effectively than pristine graphene (P-Gra) due to defect-induced electrostatic interactions, impacting DNA structure and nanomedicine applications.

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Area of Science:

  • Materials Science
  • Biophysics
  • Computational Chemistry

Background:

  • Graphene materials modulate double-stranded DNA (dsDNA) structure, aiding environmental antibiotic resistance gene removal.
  • The surface morphology of graphene is crucial, yet interaction mechanisms with dsDNA remain unclear.

Purpose of the Study:

  • To investigate the molecular interactions between dsDNA and both defective graphene (D-Gra) and pristine graphene (P-Gra).
  • To elucidate the mechanism behind dsDNA structural changes induced by different graphene surfaces.

Main Methods:

  • Molecular dynamics simulations were employed to model dsDNA interactions with D-Gra and P-Gra.
  • Analysis focused on structural evolution, binding stability, and intermolecular forces.

Main Results:

  • Both D-Gra and P-Gra strongly bind dsDNA, but induce distinct structural changes.
  • D-Gra causes rapid dsDNA unwinding and significant structural disruption via strong electrostatic interactions with nucleotides.
  • P-Gra exhibits a weaker capacity to disrupt the dsDNA structure.

Conclusions:

  • Defects on graphene surfaces are key to the significant unwinding and structural disruption of dsDNA.
  • This interaction mechanism, driven by defect-nucleotide electrostatic forces, leads to the loss of dsDNA's canonical B-form.
  • Findings support the design of engineered graphenic materials for biological and medical applications.