I'm working with a bead-beating method to get DNA from biofilm growing on Kaldnes K1 rings. I'm starting with 5 rings in extraction buffer (100 mM Tris, 100 mM EDTA, 100 mM phosphate, 1.5 M NaCl) and SDS in a bead-beating step. After bead-beating I've collected the supernatent and proceed with MoBio Powerlyzer DNA extraction kit at step 8. When I complete the DNA extraction, I can't see any DNA on a 1% gel nor quantify it with a nanodrop.
I contacted MoBio, and they had several recommendations. One of which is to alcohol precipitate the DNA to concentrate it after bead beating but before proceeding with the DNA extraction. I've found methods for ethanol and isopropanol precipitation of the DNA which typically recommend 0.3-0.5 M NaCl. Would the extra salt in my extraction buffer interfere with precipitation? Would diluting it with sterile DI water resolve the issue? Or would that complicate the issue by diluting the DNA as well? Do you have recommendations on which alcohol to use in the precipitation?