DNA binding to small anionic ligands: the case of Orange G dye.

Abstract

Here we advance in the understanding of nucleic acids interactions with small anionic ligands by characterizing the binding of the Orange G (OG) dye to double-stranded DNA via single molecule force spectroscopy. While there is no detectable interaction at low ionic strengths, we found that for [ ${\text{Na}}^{+}$ ] = 150 mM OG was able to interact with the double-helix via groove binding in a non-cooperative way, with a relatively high equilibrium association constant ( $\sim$ ${10}^5$ ${\text{M}}^{-1}$ ) that is compatible to other classic DNA small ligands. Furthermore, experiments performed with a fixed OG concentration at various ionic strengths clearly show that the binding can be turned "on / off" by regulating the concentration of available counterions, a result that can guide the development of new synthetic ligands and shows how to modulate their interactions with nucleic acids. The present work therefore advances in evaluating the fundamental role of the ionic strength on the DNA interactions with small anionic ligands.