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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.
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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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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 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.
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Supercoiling DNA with a free end.

Daniela Moretti1, Giada Forte2, Giuseppe Gonnella1

  • 1Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy. daniela.moretti@uniba.it.

Soft Matter
|February 27, 2026
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Summary
This summary is machine-generated.

Applying torque to open DNA induces supercoiling transitions. DNA shifts from a swollen to a plectonemic phase, showing non-linear twist and localized writhe dynamics, with potential for experimental validation.

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Area of Science:

  • Biophysics
  • Polymer Physics
  • Computational Biology

Background:

  • DNA supercoiling is crucial for genomic functions.
  • Understanding DNA mechanics under torque is essential.
  • Open DNA end dynamics present unique challenges.

Purpose of the Study:

  • Investigate supercoiling dynamics in open DNA under constant torque.
  • Analyze steady-state twist and writhe profiles.
  • Explore the transition between DNA phases.

Main Methods:

  • Coarse-grained Brownian dynamics simulations.
  • Mean-field theory analysis.
  • Modeling of DNA polymer under applied torque.

Main Results:

  • Observed a critical torque threshold for phase transition (swollen to plectonemic).
  • Identified non-linear, inhomogeneous twist profiles in the plectonemic phase.
  • Demonstrated diffusive twist accumulation and negligible writhe diffusion.

Conclusions:

  • DNA supercoiling is torque-dependent, even with a free end.
  • Plectoneme formation is localized near the torque application point.
  • Results provide a framework for single-molecule experiment comparisons.