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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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Single-Strand DNA Binding Proteins

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Related Experiment Video

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Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

Published on: September 27, 2024

Unwinding dynamics of double-stranded polymers.

M Baiesi¹, G T Barkema, E Carlon

¹Department of Physics, University of Padua, 35131 Padova, Italy.

The Journal of Chemical Physics

|October 26, 2010

Summary

Polymer strands unwinding from a double helix separate from the ends inward. The total unwinding time for these lattice polymers scales with length N, suggesting strands are out of equilibrium.

Area of Science:

Polymer Physics
Statistical Mechanics
Biophysics

Background:

Double-helical polymer conformations are common in biological systems.
Understanding polymer unwinding dynamics is crucial for processes like DNA replication and protein folding.

Purpose of the Study:

To investigate the dynamics of two lattice polymer strands unwinding from a double helix.
To determine the scaling relationship between unwinding time and polymer length.

Main Methods:

Simulating Rouse dynamics for two interacting polymer strands.
Analyzing the progression of unwinding from the ends inward.
Characterizing intermediate conformations and strand lengths over time.

Main Results:

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Unwinding initiates from the ends and proceeds inward.
Intermediate states feature a tightly wound core with extended loose strands (length l∼t^0.39).
The total unwinding time scales as τ(u)∼N^(2.57±0.03).

Conclusions:

The unwinding process is characterized by a distinct inward progression.
The observed scaling law provides insights into the time required for complete separation.
Theoretical analysis suggests the loose strands exist in a non-equilibrium state during unwinding.