inferring ligation site motif based on restriction enzyme
I'm trying to understand how to find out the ligation motif based on the restriction enzyme. In my data 4base cutter is used and the enzyme is MboI (^GATC), I'm reading different webpages and some suggest the site should be "GATCGATC" but I can't find an explanation how is this computed, what would happen if I used another enzyme, say HindIII. I'd appreciate any explanation of this. (this is something that is used as a parameter when running HiC-Pro)
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Cut site for MboI is shown on the NEB page here. Sequence before
GATCcan be anything. Similar site for HindIII.ok I think I figured it out why MboI ("GATC") will give a ligation site of "GATCGATC". See Fig 1b of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706059/
Based on this the ligation site for HindIII (A^AGCTT) will be AAGCTAGCTT. Or am I wrong? does having a 4bp cutter vs 6bp cutter change this?
MboI produces blunt ends. HindIII produces sticky ends. See this page.