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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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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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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

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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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Restarting Stalled Replication Forks02:37

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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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Translesion DNA Polymerases02:10

Translesion DNA Polymerases

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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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Updated: Nov 1, 2025

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
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High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

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Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations.

Valery V Prokhorov1,2, Nikolay A Barinov3, Kirill A Prusakov3,4

  • 1Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation. vprokh@gmail.com.

Nano-Micro Letters
|June 17, 2021
PubMed
Summary
This summary is machine-generated.

DNA molecules undergo significant structural changes, including kinking and melting, when interacting with charged surfaces. This reveals complex nanoscale mechanical responses beyond traditional models.

Keywords:
DNA kinksDNA surface conformationsKinetic trappingLateral stressPeriodically charged surface

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Area of Science:

  • Biophysics
  • Materials Science
  • Nanotechnology

Background:

  • The native structure of DNA is generally assumed to be preserved upon surface adsorption.
  • The impact of lateral surface forces on DNA conformation during adsorption has been largely unexplored.

Purpose of the Study:

  • To investigate the conformational changes of DNA adsorbed onto periodically charged lamellar templates.
  • To elucidate the role of electrostatic interactions and lateral stress in DNA structural anomalies.

Main Methods:

  • High-resolution atomic force microscopy (AFM) was employed to visualize DNA structures.
  • Analysis focused on DNA conformation, kinking, melting, and supercoiling on charged surfaces.

Main Results:

  • DNA molecules exhibit significant kinking, local melting, and supercoiling when adsorbed on positively charged lamellar templates.
  • These anomalies are attributed to overcritical lateral bending stress (> 30 pNnm) arising from anisotropic electrostatic interactions.
  • Surface-induced mechanical instability and the impact of helicity on DNA shape were observed.

Conclusions:

  • DNA adsorption on charged surfaces induces nonlinear, in-plane mechanical responses (bending, tensile, unzipping) beyond the worm-like chain approximation.
  • Surface-induced lateral electrostatic stress fundamentally alters DNA conformation, leading to previously unrecognized structural anomalies.
  • This study opens a new research area into anomalous kinetically trapped DNA conformations driven by nanoscale nonlinear physics.