I'm a bit confused about the effect of formaldehyde crosslinking on protein conformation (in ChIPseq experiments).
Do I understand it correctly that formaldehyde only partially denatures the proteins?
Is there any information on how resistant is such DNA-protein cross-linked state to further changes in protein conformation?
In example would the addition of EDTA to a zinc-finger protein open the DNA binding pocket and release the chromatin fragment?
What about SDS? I have heard that crosslinked DNA-protein is resistant to SDS, yet others seem to claim that SDS increases the availability of specific protein areas to antibodies in subsequent bead-binding. If so, then wouldn't SDS also alter DNA binding stability?
Looking forward to your input!
Thanks
Do I understand it correctly that formaldehyde only partially denatures the proteins?
Is there any information on how resistant is such DNA-protein cross-linked state to further changes in protein conformation?
In example would the addition of EDTA to a zinc-finger protein open the DNA binding pocket and release the chromatin fragment?
What about SDS? I have heard that crosslinked DNA-protein is resistant to SDS, yet others seem to claim that SDS increases the availability of specific protein areas to antibodies in subsequent bead-binding. If so, then wouldn't SDS also alter DNA binding stability?
Looking forward to your input!
Thanks
Comment