We want to differentiate the ssDNA and dsDNA in the solution and the simple absorption spectrum at 260/280 fails to give us the individual values. Hence we want to use organic dyes which are not commercial and have the capability to bind to only ssDNA . If there are any dyes which give a peak at a particular wavelength for ssDNA and at another wavelength for dsDNA it will be even better for our work.
GelRed® and GelGreen® can be used to stain both ssDNA and RNA, but GelRed® is about 5 times more sensitive for single-stranded nucleic acids than GelGreen®. Titration assays using a fluorescence microplate reader showed that the fluorescence signal of GelRed® bound to ssDNA and RNA is about half that of GelRed® bound to dsDNA.
Hi Vinay,
Do you know the DNA sequence?
What is the length of the ssDNA?
I don't think there is any stain that specifically stains ssDNA. But I can suggest you a way to differentiate ssDNA from dsDNA.
You can treat your sample with ssDNA specific nucleases such as mung bean nuclease or S1 nuclease. Then check your sample in electrophoresis. If you could see the bands here then it means only dsDNA is present. If the bands are disappeared it suggests the presence of only ssDNA. But here you should note that MBN and S1 do not digest any duplex regions, that includes the double stranded structures formed by ssDNA self annealing.
Hello, Vinay Bachu !
As far as I know theoretically, you can use different techniques to detect one or another damage. For ssDNA you could employ the Picogreen Quantification and for dsDNA you can use the Gamma-H2AX assay.
I hope it was helpful.
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