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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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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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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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Protein Complex Assembly02:41

Protein Complex Assembly

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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Forces Acting on Chromosomes

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During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
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Related Experiment Video

Updated: Apr 21, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

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Entropic penalties in circular DNA assembly.

Marco Zoli1

  • 1School of Science and Technology - CNISM, University of Camerino, I-62032 Camerino, Italy.

The Journal of Chemical Physics
|November 10, 2014
PubMed
Summary

This study reveals DNA circular molecule flexibility using a novel computational method. Circular DNA structures exhibit intrinsic flexibility, allowing local helix unwinding due to base pair fluctuations.

Area of Science:

  • Computational chemistry
  • Molecular biophysics
  • Structural biology

Background:

  • DNA circularization is crucial for various biological processes.
  • Understanding the thermodynamic properties of circular DNA is essential for molecular biology.
  • Previous methods struggled to accurately model the complex forces within circular DNA.

Purpose of the Study:

  • To investigate the thermodynamic properties of DNA circular molecules.
  • To develop and apply a new computational method for analyzing circular DNA structures.
  • To elucidate the relationship between sequence, conformation, and stability in circular DNA.

Main Methods:

  • A novel path integral computational method was employed.
  • Fundamental forces stabilizing the DNA molecule were treated in real space.

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Last Updated: Apr 21, 2026

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  • Base pair and stacking contributions to the classical action were evaluated by simulating twisted conformations.

    • Main Results:

    • A free energy landscape with multiple wells was obtained for short DNA sequences.
    • These wells correspond to preferred helical repeat values.
    • Base pair fluctuations induce local helix unwinding, particularly in shorter sequences, due to increased bending stress.

    Conclusions:

    • Circular DNA structures possess intrinsic flexibility.
    • Base pair fluctuations drive transitions between conformational states, leading to local unwinding.
    • The study provides insights into the entropic contributions to DNA helicoidal structure formation.