Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: Evidence for a DNA superhelix

Abstract

The location of the DNase I-sensitive sites along the DNA of the 140 base-pair nucleosome core have been determined by using DNase I to digest nucleosome cores labelled at either the 5′ or 3′ ends of their DNA. The frequency of enzyme attack at each site has also been determined from a kinetic analysis of this data. It is found that most of the sites spaced 10 n bases apart (where n is an integer) on a single strand of the DNA are attacked, but at widely differing rates. It is proposed that the pattern of relative rates of attack reflects the common protection or exposure of sites on the two turns of a DNA super helix which has about 80 base-pairs per turn and can be correlated with X-ray crystallographic studies. Furthermore, the asymmetric distribution of frequencies of attack from one end of a strand to the other can be interpreted in terms of a left-handed super helix.