# Azure A Dye Interaction with Double-Stranded DNA Can Be Modulated by the Ionic Strength: Choosing the Binding Mode

## TL;DR

This paper shows how the Azure A dye interacts differently with DNA depending on the salt concentration in the solution.

## Contribution

The study demonstrates that the binding mode of Azure A dye to DNA can be controlled by adjusting the ionic strength of the buffer.

## Key findings

- At high ionic strength ([Na+] ≳ 10 mM), Azure A binds preferentially to the DNA groove.
- At low ionic strength ([Na+] ≲ 1 mM), Azure A predominantly intercalates into DNA.
- Single-molecule force spectroscopy and gel electrophoresis confirmed these binding mode changes.

## Abstract

We study the interaction of the Azure A dye with double-stranded
DNA in phosphate-based buffers under three different ionic strengths,
showing that the effective binding mode can be modulated by this characteristic
of the surrounding buffer. For relatively high ionic strengths ([Na+] ≳ 10 mM), groove binding is the preferable mode,
while intercalation dominates for [Na+] ≲ 1 mM.
Single-molecule force spectroscopy assays were performed to determine
these binding modes and also to extract the relevant binding parameters
of the interaction in each case, resulting in a robust characterization
of the complexes formed under different experimental conditions. Furthermore,
gel electrophoresis assays were also performed to confirm the main
conclusion about the binding mode changes. The present work advances
in the characterization of DNA interactions with complex ligands,
bringing new insights into the rational development of new synthetic
nucleic acid dyes and drugs.