Koujiro Iso

Quantitative analysis of chromatin structure by circular dichroism

Abstract Quantitative analysis of the circular dichroism of nucleohistones and protein-free DNA was carried out in order to determine the structure and the role of the linker region DNA in chromatin, in terms of the conformational change of chromatin as a function of the ionic strength. It is shown clearly that the circular dichroism of Hl-depleted chromatin isolated from calf thymus is determined only by the ratio of the core region to the linker region and demonstrated by the linear combination of the spectrum of protein-free DNA and that of the nucleosome core in 5 m m -Tris · HCl, 1 m m -EDTA (pH 7.8). The calculated spectrum for the linker region in the H1-depleted chromatin was in good agreement with that of protein-free DNA. From the difference spectra between nucleohistones and protein-free DNA, it is suggested that the chromatin has an additional winding of DNA other than 146 base-pairs of DNA around the histone core. By decreasing the ionic strength to values lower than 5 m m -Tris · HCl, 1 m m -EDTA, the ellipticity of H1-depleted chromatin increased greatly between 250 nm and 300 nm while the increase was small in the case of chromatin and the nucleosome core. Nucleosomes with linker region DNA but without histone H1 also show great increase in ellipticity in this range of wavelengths as the ionic strength is decreased. Therefore, the linker region in H1-depleted chromatin plays an important role in the conformational changes brought about by changes in the ionic strength, and the conformational changes caused in the DNA of chromatin by decreasing the ionic strength are suppressed by the presence of histone H1.

Graphic display of nucleic acid structure by a microcomputer

A microcomputer program for the display of a three dimensional structure of a nucleic acid and a protein has been developed. This program can generate a wire model and a ball and stick model on a color CRT display. The phosphate atoms on the backbone, backbone, bases and all atoms can be respectively displayed. Rotation and enlargement of a partial structure is easily accomplished.

Ribbon shaped histone H4 aggregates

Abstract The self-association process of histone H4 molecules into large aggregates is highly cooperative at an ionic strength of 0.03. Carefully prepared aggregates at this ionic strength are ribbon-shaped and take the form of right-handed helices. These ribbons have a uniform width of 20.5nm. The overall diameter of the “cylinder” formed by the helix is ca. 19.5nm, the average pitch of the helices 20nm, and the mean contour length 720nm. The thickness of the ribbon is less than 3nm.