You can use mild sonication for fragments above 500kb

Our lab uses sonication (Covaris M220) for ChIP. This is likely to give you better results because it doesn't depend on accessibility of the DNA to an enzyme (which will vary according to chromatin state and could possibly skew your results.)

If you don't have access to a sonicator and increasing the amount of enzyme has not helped, you could try...

- Increasing the incubation time

- Slightly increasing the incubation temperature

- Adding more enzyme partway through the incubation, especially if you're doing it at an elevated temperature

- Checking the buffer conditions (try adding more magnesium)

You have to standardize it...I used sonication for chromatin shearing. You can standardize the shearing by sonication at different time points and check the pulse too..

Laura Leighton Sumit K Singh Mangala Priya Viswanathan thanks for your suggestions.

I did sonication, and then increased the enzyme amount but still there is unfragmented chromatin in the gel. Since I afraid the chromatin damage by high sonication time, I do not know how long is the maximum optimized time for sonication. If you have any successful experience I would appreciate it if you explaine it.

I would not go above 60% amplitude for 30seconds with continuous pulse