The Linking Number Paradox of Nucleosomes

The Linking Number Paradox of Nucleosomes

A paradox is raised by the structure of nucleosomes. As mentioned, the DNA in eukaryotic cells is wrapped around nucleosomes. DNA in the B conformation wraps about 1.8 times around a core consisting of pairs of the four histones, H2A, H2B, H3 and H4. In the

presence of the histone H1, the wrapping is extended to just about two complete turns. This histone both serves to complete the wrapping as well as to connect from one nucleosome to the next. Superficially, the

wrapped nucleosome structure appears to possess two superhelical turns, and yet when the protein is removed, the DNA is found to possess only about one superhelical turn for each nucleosome it had contained.

One explanation for the paradox could be that the path of the DNA between nucleosomes negates part of the writhe generated by the wrapping. Because electron microscopy suggests that the connection from one nucleosome to the next is regular, tricky topology connecting nucleosomes seems not to be the explanation.

Another explanation for the paradox is that while the DNA is wrapped on the nucleosome, it is overwound. Upon removal of the nucleosome, the winding of the DNA returns to normal, reducing the twist of the DNA, so that writhe or negative supercoiling is reduced in magnitude from an average of two per nucleosome to an average of one negative superhelical turn per nucleosome. The linking number, twist, and writhe might be the following while the DNA is wrapped on one nucleosome, Lk = 20, Tw = 22, Wr = -2, and after removing from the nucleosome, the same DNA might have the following values, Lk = 20, Tw = 21, Wr =-1. The evidence, in fact, suggests this is part of theexplanation.

Analysis of the sequences of DNA found on nucleosomes indicates that the bends introduced by runs of A’s as described earlier tend to lie with the minor grooves of such runs in contact with the nucleosomes. Thus nucleosomes appear to bind to DNA to regions that already are partially bent. Analysis of the locations of these runs of A’s shows that they are spaced an average of 10.17 base pairs apart, not 10.5 base pairs apart. This then partially, but not fully, explains the linking number paradox. When this overwound DNA returns to its natural twist of 10.5 base pairs per turn, part of the supercoiling is eliminated. Although this reduces the supercoiling discrepancy, a new question is raised about the cause of the overwinding of the DNA.