Chicken erythrocyte nucleosomes have a defined orientation along the linker DNA--a scanning force microscopy study

The orientation of nucleosomes was investigated using scanning force microscopy (SFM) of hypotonically spread chicken chromatin. A virtual cross section parallel to the substrate at half maximum height of the nucleosomal structure revealed an elliptical shape. The orientation of the major axis of this ellipse was investigated in reference to the direction of the axis of the nucleosomal chain. An alignment of the nucleosomes along the nucleosomal chain was observed, with more than 50% of the nucleosomes aligned with the long axis of the chain within < or = 30 degrees deviation. The alignment distribution peaked at 10-20 degrees. The application of SFM-based image processing for the structural investigation of a protein-DNA complex demonstrates the potential for this approach in structural molecular biology.