I was extracting DNA from Paraffin slides, and after adding xylene, a thick viscous liquid formed on top of the solution, so thick I can't pipette.
Any ideas of what it could be?
You've probably dissolved the paraffin with the xylene. You need to remove the paraffin by heating followed by multiple rounds (2 or more) of washing in xylene to remove the paraffin prior to trying to do your extraction. However, you may need to do something more aggressive to extract and recover the DNA. There are protocols availble in the literature addressing these issues.
Good Luck!
So you think that just by dissolving the paraffin with xylene, you can make this thick thing? I have a good protocol, I've done this several times, but I've never seen it before!
Paraffin's a wax (i.e., long chain polymer), so yes, it could be fairly thick if it isn't sufficiently dilute and/or warm under the conditions that you are doing the work with this particular set fo slides. On the other hand, maybe the paraffin is fully dissolved and you've extracted a large amount of nucleic acids from the samples, and this is your "thick" solution. Without some additional infomation to go on, it may not be possible to differentiate between these two possibilities.
You may be able to pipette by cutting the end off the tip to get a larger hole. Use cotton wool, glass wool, or pipette tips with filters, to avoid "suck-back" problems.
Xylene may have reacted with the slides.....it once hapend with me with tissue culture plates....
Xylene concentration in the emulsion solution
increases, this invariably causes a viscosity increase. It may be due to the pipette as sally mentions above .I would use a pipette with filiters it does reduce "suck back" re: Sally.
good luck!
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