DRAQ5 (Deep Red Anthraquinone 5) is a cell permeable far-red fluorescent DNA dye which is modified anthraquinone product- 1,5-bis{[2-(di-methylamino) ethyl]amino}-4, 8-dihydroxyanthracene-9,10-dione, that can be used in live or fixed cells [2]. It is stable at room temperature, stable under normal lighting conditions and soluble in water at biologically compatible pH. It has shown to cause microscopically detectable changes of nuclear architecture for example partial unwinding of the DNA double helix by detachement of histone H1.
I could not find the exact mode of action of this chmical to DNA bases.
It is a DNA intercalator. That is probably why it affects the winding of DNA.
https://www.biolegend.com/en-us/products/draq5-9674
Hello Mr. Shapiro,
You are right it interacts with DNA.
I could find that it is membrane permeable (but how?) DNA intercalator (why it goves color only after intercalation?)
There are many DNA intercalators that show an increase in fluorescence when DNA-bound. Ethidium bromide is the most well-known one. Some of these are part of kits for DNA quantitation, such as PicoGreen. I do not know all the physical chemistry that determines why the fluorescence intensity increases upon intercalation. In part it may be due to shielding from quenching by water. In part it may the change to a more hydrophobic environment. In part it may be due to the realignment of the electronic structure of the compound.
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