Hi，is there anyone who had done 3C using plasmids instead of BAC clone?
Should I worry about the ligation efficiency between cutted plasmids (~3.2Kb)?
Hi Xi Yuan,
A long time ago I constructed a 3C control template that consisted of both plasmids and BACs (see attached paper).
The structure of BAC and plasmid DNA is essentially the same, so there is no reason to expect a difference in ligation efficiency.
Important though: are you planning to do a 'true' 3C experiment, or will this be to construct a random ligated 3C control template? If you want to do a 'true' 3C experiment, you should keep in mind that cross-linking of plasmids (and BACs) is very different from normal genomic DNA. For a random template, you do not need to cross-link. In this case, you want to do your ligation under very concentrated conditions to promote inter-fragment ligation (small reaction volume), instead of the diluted conditions used in normal 3C.
Article Transcription and Chromatin Organization of a Housekeeping G...
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