Need urgent help with DNA crosslinking!!

[jeniffer lopez]

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Hey guys!
I just wanted to know if I could use some of your genius and expertise. I have been trying to run ChIP assays but I don't get my DNA to be the right size (below 1000 bp) even though I have changed the sonication conditions to be rather loooong. Has anybody tried this before? What sonicator did you use? I am using one of those Fisher sonicators that has a long probe.
You guys are my last resort. No one else I know is doing this around here.
Thanks!!!

 

[Neuronix]

How do you know what size your fragments are? Are you running them out on an agarose gel to check? I assume you're really sonicating the hell out of them at this point and not getting the amount of chopping that you want? If this is the case, could you tell us what the longest amount of time and power (is that a model with a 1 - 10 knob) you've tried?

Good luck!

 

[jeniffer lopez]

Thanks for the quick reply!
I am sonicating at 5 (which is the max intensity my probe can take) 7 to 8x for 30''. The company recommends 4 times but with a different sonicator and I don't know if that is the problem. I have been running the agarose gels and I get pieces way above 1000 and then some smaller. I would love to get more uniform results.