Hi there,
Do you mean you lose your DNA during ethanol precipitation in the presence of 0.3M AcNa? Usually this technique is pretty efficient however the yield will highly depend on the amount of DNA to be precipitated. If low DNA content then DNA carrier should be added (tRNAs or glycogen). If problematic then silica column step may be considered (just like in DNA purification kits).
The amount of DNA is low or the kit donen't separate your DNA like you wish. It´s depend of the kit you need to prepare the sample previously.
You can alternatively use 0.3M ammonium acetate. Incubate the samples -80. Lower temperature enhances the precipitation of the DNA
You could try paramagnetic SPRI beads
THey work very well. I use them for NGS prep. There is little loss of material.
Here some theory:
http://core-genomics.blogspot.it/2012/04/how-do-spri-beads-work.html?m=1
Here the Place to buy:
http://www.beckman.it/nucleic-acid-sample-prep/purification-clean-up/pcr-purification?geolocation=it
A SpeedVac might help, it's like a combination centrifuge and vacuum where tubes are kept open.
We routinely use 0.1 volume of 3M (not 0.3M) sodium acetate. alternatively we use 1.2M NaCl. Haven't tried with less concentrated salt but it is a detail you might want to check up. Also, try adding at least 2 volumes of ethanol.
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