Re: How Ethidium bromide acts on ssDNA and dsDNA?

Dear Muhammad, your question is heard every other day in research labs. The consensus is that ethidium bromide intercalates in double stranded DNA at every 2.5 base pair or so. There is an existing crystal structure in which ethidium bromide is complexed with a ribo CpG dinucleotide that shows this arrangement. This can be found in a recent discussion done by Ewen McLaughlin in this forum.

Moreover, ethidium bromide can also bind to single-stranded DNA and RNA. According to Sambrook et al, ethidium bromide binds to regions having an helical character that is mainly caused by intramolecular interactions. This is not far-fetched since it is known that single-stranded nucleic acids often form various helical regions, and this is where ethidium bromide could preferentially bind.

Hope this helps,

Daniel