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Are there any commercially available fluorescent dyes that will bind only to double stranded DNA (not RNA, single stranded DNA etc.) for studying in vitro using confocal microscopy?

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Most of the dyes used for visualization bind with a much higher affinity to dsDNA. This would be SybrGreen, EtBr (although this will bind RNA as well). There is a pretty comprehensive website from Life Technologies about Nucleic acid stains that is worth a look.

There is as well a publication on this topic: "DNA Staining for Fluorescence and Laser Confocal Microscopy"

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  • $\begingroup$ YOYO, TOTO join the list, I believe they have 1000-10000x binding/fluorescence efficiency in presence of dsDNA than ssDNA $\endgroup$ – aaaaa says reinstate Monica May 9 '15 at 6:06
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You may also want to look at acridine orange. It binds both single stranded and double stranded DNA, but fluoresces green when bound to double sided DNA, and orange when bound to single stranded DNA/RNA, making it very easy to see both in the same image.

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