For "short" times, no. For "longer times", yes. Are the particles agglomerated or aggregated? Were they dried and you are trying to redisperse them?

Omar Gonzalez-Ortega

Thank you for your response.

After centrifugation and discarding the supernatant, the precipitate should be dispersed in the water by adding some distilled water, and this is not done well by vortexing. Therefore, I want to know whether dispersing with an ultrasonicator does not damage the nanostructure and the RNA inside it.

If vortexing works keep doing it like that. A bath sonicator can also be used. Even an ultrasonic tip can be used but for a couple of seconds.