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does sonication alter the DNA, aside from becoming fragmented? So that there could occur problems with procedures, that normally work on isolated DNA?
What procedure are you trying to do?
Sonication applies energy to DNA so it vibrates and snaps. Where it snaps is random, it may leave sticky ends or blunted ends. I'm not aware of any information that suggests sonication can change the properties of DNA at a fundamental level. High power sonication and excessive heat (which can be generated during the procedure) can however alter protein conformation - could your problem relate to the presence of proteins on DNA rather than the DNA itself, or are you sonicating pure DNA?
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