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As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.

I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

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My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.

This is a follow-up question to this one, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.

Any ideas?

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With specific attention to more efficient ligation (e.g., after restriction enzyme digestion), there are commercial products on the market that use a modified topoisomerase to catalyze such a ligation. – user560 Apr 14 '14 at 19:25

I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

Cohesin binding is not motif dependent (like transcription factors) and is also dynamic. Though sequence may have a role it is, just as in the case of nucleosomes, mostly the overall composition rather than a sequence based motif:

From this article:

Cohesin binding peaks correspond closely to peaks of high local AT composition, a base composition periodicity of ∼15 kb that is distinct from the ∼50 kb periodicity of base composition isochores, consistent with axis association of cohesins.

DNA-protein complexes can be crosslinked and subsequently the loops can be pulled down. However, this is tricky. You would need to cut the DNA at the loop ends in order to ligate them together. I don't know how to do that (Perhaps by using an antibody linked to an endonuclease).

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