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Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak signal, even a low emission would disturb the reading.

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    $\begingroup$ I don't understand why you want to dye the DNA at the same time as performing the Raman spectroscopy, anything else you put in your sample will interfere in some way during your measurements, I assume. Does the dye need to be specific for DNA, or is a general nucleic acid dye enough? Should it be a non-covalent dye or something your want to specifically attach to a certain position in your DNA? $\endgroup$ Feb 2, 2012 at 13:11
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    $\begingroup$ The Dye is needed to know where to aim. The Signal form the dye can be subtracted by measuring it without DNA. The main thing of importance is that the Signal is not so strong that it overshadows the DNA signal. $\endgroup$
    – Uli
    Feb 2, 2012 at 13:40

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One option is to use biotin labelling. Most molecular biology supply companies do kits for this, and supply biotinylated nucleotides.

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  • $\begingroup$ I accepted your answer, but I don't really know how well it would have worked, as the experiments were never performed after all. (It was a colleagues project, not mine) $\endgroup$
    – Uli
    Mar 21, 2012 at 13:14
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Methylene blue? Certainly not as sensitive or specific as other options but it's cheap and does not fluoresce.

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