Measuring the geometry of DNA grooves

We present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate-phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis.

Chromatin reconstitution on small DNA rings. III. Histone H5 dependence of DNA supercoiling in the nucleosome

Mononucleosomes were reconstituted on small DNA rings in the presence of histone H5 and relaxed to an equilibrium using calf thymus topoisomerase I. DNA products, when compared to the equilibria observed with the same minicircles in the absence of histones, showed that a linking number reduction of 1.6 to 1.7 was associated with this reconstitution, in contrast with the 1.1 to 1.2 figure reported in our recent study of the H5-free nucleosome. Gel electrophoretic properties and electron microscopic visualization of the nucleosomes suggest a correlation between this increase and a further wrapping of the DNA around the histone core from less than 1.5 turns of the superhelix in the absence of H5, to close to two turns in its presence. Implications for DNA topology in chromatin are discussed.