In the direct manual DNA extraction from bacterial cells DNA has to be in the supernatant, but were you amused to see at times DNA being only along with the sediment?
For Gram negative bacteria the procedure usually followed: Single bacterial colony from an overnight grown culture was suspended in 100 µl of sterile MilliQ water and boiled for 5 minutes. The suspension was centrifuged at 8,000 rpm for 10 min. The supernatant containing bacterial DNA was used as template for PCR.
Not sure I understand your question but i guess what happens is you have gDNA forming H bonds with lipids and proteins from the membrane and that's why it precipitates down. Also I don't understand why you boil and spin for so long unless you are working with Chuck Norris bacteria that will not lyse otherwise. Try next time to microwave the suspension for 20 sec then centrifuge for no more that 3min. You'll be good to go for PCR.
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