Hi there,

Sonication is certainly breaking DNA, it has been the method of choice for shearing genomic DNA into fragments... The result will depend on the settings used

If your oligos are bound to nanoparticles the amount of damage they would receive from sonication would depend on if they are short enough to bind to only one nanoparticle (less shearing) or if they are binding to two or more nanoparticles (more shearing).

The damage that DNA sustains from sonication is essentially due to the DNA strands tearing. If they are affixed to a nanoparticle, this greatly reduces the amount of movement that the DNA molecule is able to do.

First: oligos are much much shorter than genomic DNA, or even plasmid DNA. So i would not be too worried about that sonication step.

Second, a good way too ascertain the integrity of your oligos through sonication might be to run them in an agarose gel afterwards. That is: if they are neither covalently bound to your nanoparticles, nor bound through some sequence specific strong interaction, you could detach them with a strong polyanion competitor such as heparin.

Hope this helps.

Charles