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Related Experiment Video

Updated: May 27, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

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Published on: April 26, 2013

Bubble statistics and positioning in superhelically stressed DNA.

Daniel Jost¹, Asif Zubair, Ralf Everaers

¹Laboratoire de Physique and Centre Blaise Pascal of the École Normale Supérieure de Lyon, Université de Lyon, CNRS UMR 5672, Lyon, France.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|November 9, 2011

Summary

Superhelical stress in DNA causes large, cooperative bubble openings, significantly more than in unconstrained DNA. Genomic DNA, unlike random sequences, shows increased bubble formation near transcription start sites.

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

Biophysics
Computational Biology
Genomics

Background:

DNA's double helix is thermodynamically stable but can denature.
Superhelical stress, a torsional force, can influence DNA structure and stability.
Understanding DNA denaturation under stress is crucial for various biological processes.

Purpose of the Study:

To develop a computational framework for studying DNA denaturation under superhelical stress.
To calculate sequence-dependent DNA bubble opening probabilities.
To compare denaturation in genomic versus random DNA sequences.

Main Methods:

Utilized transfer-matrix solutions of the Zimm-Bragg model for unconstrained DNA.
Employed a self-consistent linearization of the Benham model for superhelical DNA.
Analyzed large sequences (10^6-10^9 base pairs) for numerical efficiency.

Main Results:

Superhelical DNA exhibits highly cooperative bubble openings (10^2-10^3 base pairs) at physiological conditions.
Bubble sizes are orders of magnitude larger than in unconstrained DNA.
Genomic DNA shows a higher propensity for large bubble formation compared to random sequences with similar GC-content.

Conclusions:

Superhelical stress significantly enhances DNA bubble formation, with implications for DNA mechanics.
Sequence disorder influences bubble localization and statistics in heterogeneous DNA.
Genomic DNA's specific sequence composition predisposes it to large bubble formation upstream of transcription start sites.