Dear community
I will have access to a HiC dataset that investigates if a short mechanical stimulus of less than a minute leads to an alteration in chromatin conformation in human cells. The cells have been fixed with 2% formaldehyde. The samples, originating from the same cell culture, have been fixed right before and right after the stimulus, so less than a minute apart. I am wondering if any confirmation effects originating from the stimulus will be detectable, which depends a lot on the formaldehyde fixation kinetics.
There have been some studies on the kinetics for DNA-Protein interactions which is in the range of seconds for high formaldehyde concentrations. As far as I know there have not been similar investigations on crosslinking kinetics for DNA-DNA interactions. Manufacturers of HiC kits usually recommend fixation for several minutes (ArimaKit: 10 minutes) but it is unclear if this length has been chosen to "freeze" the conformation of DNA or to provide sufficient protection the sample from degradation.
Does anyone know if crosslinking of DNA-DNA interactions with formaldehyde (in a typical concentration for HiC experiments) happens on the timescale of seconds or rather minutes?
Thank you!
