Abstract
We use Förster Resonant Energy Transfer (FRET) in order to measure the increase of flexibility of short ds-DNA induced by the intercalation of dipyridophenazine (dppz) ligand in between DNA base pairs. By using a DNA double strand fluorescently labeled at its extremities, it is shown that the end-to-end length increase of DNA due to the intercalation of one dppz ligand is smaller than the DNA base pair interdistance. This may be explained either by a local bending of the DNA or by an increase of its flexibility. The persistence length of the formed DNA/ligand is evaluated. The described structure may have implications in the photophysical damages induced by the complexation of DNA by organometallic molecules.
Highlights
The number of DNA base pairs is limited by the range over which the Förster Resonant Energy Transfer (FRET) can take place that is approximately 10 nm
The most important factor we care in FRET process is the transfer efficiency, that relies on two assumptions
We have a mixture of uncomplexed DNA and DNA strands complexed with one ruthenium molecule
Summary
Since the first observation of the molecular “light switch” effect of Ru(bpy)2dppz2+for DNA their interaction with DNA has been intensively studied (Friedman et al, 1990; Brennaman et al, 2002, 2004; Hu et al, 2009; Lim et al, 2009; Klajner et al, 2010; Sun et al, 2010; Song et al, 2012; Vidimar et al, 2012). Both complexes Ru(bpy)2dppz2+and Ru(phen)2dppz2+ have served as “molecular light switch” for DNA, luminescing intensely in the presence of DNA but with no photoluminescence in aqueous solution and can be seen as unique reporters of nucleic acid structures (Song et al, 2012). Intercalated complexes are located in the minor groove, stabilized by extensive ancillary interactions (Erkkila et al, 1999) This discrepancy notwithstanding, the crystal structure attests the remarkable structural flexibility of DNA upon high-density ligand binding, and illustrates the nuanced binding geometries sampled by a non-covalently bound small molecule. It highlights the dominance of metalloinsertion as the preferred binding mode to destabilized regions of DNA
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