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Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.

Pauline J Kolbeck^1,2, Miloš Tišma³, Brian T Analikwu³

¹Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany.

Nucleic Acids Research

|November 24, 2023

Summary

We developed a quantitative model to understand how DNA topology affects molecular binding. This model accurately predicts binding changes in supercoiled DNA, crucial for various biological and technological applications.

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Area of Science:

Biochemistry
Molecular Biology
Biophysics

Background:

DNA binding is influenced by mechanical strain and local structure.
DNA topology, including supercoiling, imposes global constraints on binding.
Understanding these constraints is vital for DNA applications.

Purpose of the Study:

To present a quantitative model for DNA topology's effect on binding.
To enable straightforward numerical implementation of the model.
To investigate fluorescent intercalator binding to DNA.

Main Methods:

Developed a quantitative model for topology-modulated DNA binding.
Utilized fluorescent intercalators for DNA unwinding and fluorescence detection.
Validated the model with bulk experiments and single-molecule assays.

Main Results:

The model accurately describes bulk experimental data across various conditions.
Demonstrated and quantitatively modeled supercoiling-dependent binding in single-molecule assays.
Observed direct correlation between DNA supercoiling and intercalator density.

Conclusions:

DNA topology significantly modulates molecular binding.
The model provides a robust framework for predicting binding behavior.
Findings have implications for DNA detection, quantification, and cellular binding modulation.