Hi, I just checked Dynabeads manual and it says 4 wash steps are enough. Did you try reducing washing steps?

I had previously tried to do 4 washes, but couldn't get results from the ChIP.

I decided to increase the washing, but to keep each wash to check if I'm losing my bound DNA. 

Unfortunately, I did not save the washes during the previous experiment, so I can not check if there was amplification in any of the 4 washes. 

However, the results (or lack of) seem quite similar. 

Maybe the lack of results after 4 washes was due to poor DNA binding to your antibody/protein, not because it was something wrong with the wash. Try increasing time for binding, that might help. And of course double checking if the antibody/protein is still working as expected woudl be good.

Actually, I had not mentioned this, but I actually did prolong the incubation of the bead/Ab and sample when I carried out the 6 wash procedure - I left the samples to incubate with the beads/Ab, with rotation, over night. 

Dovydas, 

What do you do with the wash flow through to check if you are loosing the bound DNA. Do you reverse the crosslink and RNAse treat before extracting the DNA and running on agarose gel or qPCR?

I am having the same problem but don't know what step to check (i am using sepharose beads though)

I saved each wash in a separate tube and treated them as if they were regular samples - I continued to reverse cross-link them, extract DNA by phenol-chloroform extraction , run a regular PCR and visualize the product by running on an agarose gel.