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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Binding interaction between polycyclic aromatic compounds and DNA by fluorescence displacement method.

Yin Wei¹, Liang-Hong Guo

¹State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China.

Environmental Toxicology and Chemistry

|August 4, 2009

Summary

This summary is machine-generated.

Polycyclic aromatic compounds (PACs) bind to DNA primarily through intercalation, not groove-binding. Peripheral polar groups on PACs are more critical for DNA binding affinity than the number of aromatic rings.

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Area of Science:

Environmental Chemistry
Molecular Biology
Toxicology

Background:

Polycyclic aromatic compounds (PACs) are environmental pollutants known to interact with DNA.
Understanding the noncovalent interaction of PACs with DNA is crucial for elucidating their genotoxic mechanisms.

Purpose of the Study:

To investigate the DNA-binding interactions of 15 different PACs.
To determine the binding modes (intercalation vs. groove-binding) and affinities of PACs with DNA.
To explore the structure-activity relationship between PAC chemical structure and DNA binding.

Main Methods:

Fluorescence displacement assay using DNA-binding dyes (thiazole orange, Hoechst 33258, DAPI) as probes.
Viscosity measurements to assess DNA conformation changes.
Determination of dissociation constants (Kd) for PAC-DNA interactions.

Main Results:

PACs, including 1-hydroxypyrene, 1-aminopyrene, and 1-pyrenebutyric acid, predominantly interact with DNA via intercalation.
Dissociation constants varied, with 1-hydroxypyrene showing the highest affinity (0.62 microM).
Peripheral polar groups on PACs significantly influenced DNA binding affinity more than the number of fused aromatic rings.

Conclusions:

The fluorescence displacement method is an effective tool for studying PAC-DNA interactions.
PACs primarily intercalate into DNA, and their binding affinity is modulated by peripheral polar substituents.
This study provides insights into the molecular mechanisms underlying PAC genotoxicity.