Do you have an assay for crosslinking, with a goal?

You might try reducing formaldehyde. Reducing pH will have a similar effect on the protein crosslinking chemistry.

Hello Junfeng Jiang

You may use a catalyst that can catalyze the removal of adducts and/or crosslinks under relatively mild conditions (conditions that are not as damaging to biological samples as the conditions used by other methods of crosslink removal). Other methods use high temperatures and are carried out at pH that are damaging to biomolecules such as nucleic acids and proteins.

This method can be carried out in relatively mild conditions (pH near neutral, temperature near room temperature, short time frame of treatment, etc.), and inflict less damage on biomolecules present in aldehyde fixed samples.

Attached below are links that may help!

https://patents.google.com/patent/WO2018219997A1/en

https://patents.google.com/patent/US20170283860A1/en

Best.

Malcolm Nobre John Carter

Thanks for the solution.

To clarify the question more clearly, I need to reduce the cross-linking of the original FFPE sample, which will be used as the starting material of the HIC experiments.

Since the FFPE samples fixed with 10% FA, the samples could not be fully digested by restriction enzymes, researchers used protein K or ultrasonic to reduce the cross-linking level, while still keeping the cross-linking level (2% for example) to maintain the chromatin structure for downstream HIC analysis.

Best,

Junfeng

Ah. You have no control over the sample fixation process. You're stuck with what you have, and they're too highly cross-linked, already.

In that case I know no methods other than what you listed. I suggest you try a range of concentrations for each of those remedies.

Good luck.

John Carter

Thanks for suggestions.