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Part of the answer is the Histones (spools for DNA) https://en.m.wikipedia.org/wiki/Histone

There are other protein complexes that keep the strand in proper shape and form. They unfold the strand periodically, and can cut and repair it as needed.

If my mind serves me correctly, it is part of gene regulation. Genes located in places of the strand that tend to form tight knots are "more difficult" to transcribe, so they express less, to some extent.






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