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In order to make easy and low-cost experiments, we are searching for natural dyes (or easy to make) that can color DNA, instead of for instance Ethidium Bromide that is hard to find and is expensive.

We are new to this field, but we learned that DNA dyes need to intercalate in between DNA bases. To do so, the molecule must be preferably poly-cyclic, aromatic and planar.

So the question is, is there any chemical that can be readily used for this purpose or if not, any lead about a molecule that can be easy to find by anyone.

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    $\begingroup$ Rhodamine dyes are very cheap (used as dyes in fishing and easily purified) or you could synthesise some porphyrin. $\endgroup$
    – porphyrin
    Commented Jul 26, 2018 at 8:39
  • $\begingroup$ Thank you both for your answers. Clarification: we are trying to get dyes that can be used by children or non-scientific persons. Methylene blue might be the best option, but we are trying to get even more accessible chemicals, like lawson, cephalopod ink or beetroot (we did not try them yet). $\endgroup$
    – HBallot
    Commented Jul 27, 2018 at 7:32
  • $\begingroup$ In that case why not try some food dyes or writing inks. You can probably look up their structures on line and choose flat aromatic types that can intercalate, although binding is also possible in the major and minor grooves. $\endgroup$
    – porphyrin
    Commented Jul 28, 2018 at 12:48

2 Answers 2

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Though not a naturally occurring dye, methylene blue has been used as a DNA stain. It is inexpensive and readily available. It is also comparatively nontoxic, and is used as a medication in pisciculture, so it can be found in pet stores.

If you choose to use methylene blue, save some for the blue bottle demonstration, a sensitive test for oxygen. Vitamin C or other reducing agents can be used instead of glucose.

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Ellipiticine is a molecule that meets most of your criteria.
George Watson / CC BY (https://creativecommons.org/licenses/by/4.0)

  1. a "natural" molecule, produced by trees native to Hawaii and/or Australia. It therefore meets your ask for "natural" molecules.

  2. a DNA intercalator, binding to the major groove of the DNA helix.

  3. a UV absorber whose spectrum changes on binding DNA.

  4. a fluorophore whose fluorescence properties are modulated by solvent and/or binding to DNA.

However it is not easy to get. Ethidium bromide is probably easier.

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