inferring ligation site motif based on restriction enzyme
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2.5 years ago
a.abnousi ▴ 30

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)

HiC-Pro • 1.1k views
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Cut site for MboI is shown on the NEB page here. Sequence before GATC can be anything. Similar site for HindIII.

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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?

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MboI produces blunt ends. HindIII produces sticky ends. See this page.

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