Hey everyone, is it possible to use sonication to break only base pairs but not phosphodiester bonds?
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I doubt it. The energy required to melt DNA or denature RNA is generally enough for phosphodiester bonds to start breaking (as evidenced by the fact that DNA and RNA don't store well at any temperature close to melting temperature). Sonication is commonly used for shearing DNA (at the phosphodiester bonds) for next-gen sequencing, which wouldn't work if the bases routinely broke from the phosphate/ribose backbone. I don't have a lot of experience with sonication, though, so I could be wrong.
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