With the ChIP protocol there are two washes performed, one with a buffer that has the following ingredients:
Tris-HCl pH 8
EDTA
NaCl
Triton X-100
SDS
and the other which has the following:
Tris-HCl pH 8
NP-40
LiCl
sodium deoxycholate
What is the purpose of changing the salt used?
Hi,
From the millipore FAQ (http://www.millipore.com/catalogue/item/17-371#)
What is the purpose/chemistry behind the use of LiCl and NaCl in the wash buffers ?
" The use of different types of salts improves the effective removal of non-specific chromatin interactions with the agarose beads. Lithium is also soluble in buffers containing high amounts of SDS. "
Hi,
From the millipore FAQ (http://www.millipore.com/catalogue/item/17-371#)
What is the purpose/chemistry behind the use of LiCl and NaCl in the wash buffers ?
" The use of different types of salts improves the effective removal of non-specific chromatin interactions with the agarose beads. Lithium is also soluble in buffers containing high amounts of SDS. "
The reason that NaCl doesn't play nice with SDS is because you'd be adding extra sodium to the sulfate in SDS-- no fun.
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