Dear All,
I am doing ligation of the padlock probe. The efficiency is pretty good (more than 90%). But I have a very simple question about this process.
As shown in the following figure, in normal ligation process of a padlock probe, a single padlock probe is circularized by ligase. But according to simple math, events like two padlock probes are ligated in a head-to-tail fashion should also happen.
So I just wander, why the ligation process does not go on according to the theoretical probability, but insteand, prefer a intramolecular circularization reaction?
Best regards
Binbin
I've never done a padlock probe ligation, but I suspect that circle formation vs dimerization is an issue of concentration: at lower probe concentration, circle formation is favored, at higher probe concentration, dimerization is favored. I saw similar effects in blunt end ligations of cloned fragments into plasmids, which do tend to be done at higher DNA concentration that staggered end ligations.
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