enzymes that stabilize DNA loops
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).