DNA supercoiling and its effects on the structure of DNA

In prokaryotic organisms, there is strong evidence that the DNA is underwound or negatively supercoiled. The degree of supercoiling of intracellular DNA is less certain, and various estimates that can be made from existing data place the specific linking difference (superhelical density) of intracellular DNA in prokaryotes around -0.04. The effects of negative supercoiling on DNA structure are illustrated by the flipping of alternating C-G or T-G sequences from right-handed B-helical form to the left-handed Z-helical form. For a plasmid containing a 42 base-pair alternating C-G insert, the B-to-Z transition occurs at a specific linking difference of 0.031 in a dilute aqueous buffer; the same transition occurs at a specific linking difference of -0.041 for a plasmid containing a 42 base-pair alternating T-G insert. The probing of the structure of a particular sequence of intracellular DNA is discussed.