pattern of DNA precipitation - (Jul/20/2006 )
sometimes I found in my DNA ppt in the bottom, and sometimes in the body of the eppendorf tube. Can someone please explain me the reason behind it??
It probably depends various factors including the type of tube, the angle of the slot in the rotor, the amount of DNA, the % EtOH you use, how long the spin lasts and the length of spin..
Most of the time I use non-stick tubes and find the DNA nicely pelleted at the bottom. However in one application when I use standard tubes and a shorter spin I often find more of a smear down the side.
Also if you use carriers (like poly(dIdC)-poly(dIdC) and glycogen you will end up with a heavier complex which should be more likely to accumulate at the bottom of the tube not down the side.
i always use same tube (1.5ml eppendorf tube). like 12 sample i centrifuge in 14K rpm for 10 min. and I get ppt in the bottom in some tube and in the wall/body of some tube
i've noticed that it depends of the way you're precipitationg your DNA.
By using etoh, pellet is at the bottom of the tube.
By butanol, pellet is also on the side of the tube. guess that the clumps are bigger with butanol and so the acceleration rates is sufficent to have moving of DNA at low speeds... (with buoh, 1000rpm is enough...)