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Why do only some nuclear lysis buffers create DNA 'goop' - (Feb/07/2013 )


There is a goopy snotty DNA substance that appears after lysing cells in some nuclear lysis buffers (like buffer from ChIP kits), but not with other lysis buffers (like buffers for collecting the nuclear fraction of protein/nuclear extraction). It appears you can lyse nuclei without creating DNA "goop", so what causes it sometimes and not other times? Where does the DNA disappear to when collecting nuclear fractions?

Buffer components
ChIP nuclear lysis buffer:
1% SDS
50mM Tris, pH 8.1

Nuclear extract lysis buffer:
1M HEPES, pH 7.9
5M NaCl
25% Glycerol



This is a typical problem, to avoid that:

-keep on ice at all times
-vortex instead of pipetting up and down if you can
-if you see sticky DNA in the end just add 1-2 ul DNase at RT, it always works better than sonication for us