I need to know the risks of using sonication for my bacterial DNA. If I could use this, what time and frequency is necessary to sonicate in my bacterial samples?
No, you cannot. Proteinase K is used to hydrolyze proteins to small peptides and aminoacids, facilitating cell lysis, breaking down DNA-binding proteins, etc. Sonication, on the other hand, has nothing to do with deproteinizing; it will fragment your genomic DNA and decrease its average size (dramatically) to an extent determined essentially by the amount of time under sonication and the power and geometry of the sonication probe.
In the context of purifying genomic DNA, you might use sonication for cell lysis, but the quality of the resulting preparation will suffer. Most recipes for genomic DNA preps use gentler lysis methods (lysozyme, lysostaphin, EDTA and the like).
No, you cannot. Proteinase K is used to hydrolyze proteins to small peptides and aminoacids, facilitating cell lysis, breaking down DNA-binding proteins, etc. Sonication, on the other hand, has nothing to do with deproteinizing; it will fragment your genomic DNA and decrease its average size (dramatically) to an extent determined essentially by the amount of time under sonication and the power and geometry of the sonication probe.
In the context of purifying genomic DNA, you might use sonication for cell lysis, but the quality of the resulting preparation will suffer. Most recipes for genomic DNA preps use gentler lysis methods (lysozyme, lysostaphin, EDTA and the like).
Alejandro is correct - you will end up with bacterial DNA ~200 bp with extended sonication and useless for most applications unless you are doing short sequence PCR. Most extractions using chaotropic reagents - phenol guanidinium salts are good at getting rid of protein. However with gram-positive bacteria there is often a problem with lysing them in the first place.
Ian Teo
I have used sonification for cell lysis in the past, but that was not a success. Using Proteinase K as was said earlier will give much better results.
have you tried glass beads until now? you can use glass beads as mechanical way to disrupt the cell wall. if you don't access to Pro K, I think this method will be helpful.
Try adding SDS. It can be a alternative replacement for proteinase K, as SDS can also denature the protein.
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