ABSTRACT
Chromosome structures exhibit different levels of complexity.
The most fundamental structures are built by a simple DNA
interaction with small basic proteins and have been elucidated by
biochemical investigations and X-ray crystallography [1-4]. Higher-
order structures are difficult to analyze and have often been
approached with the help of electronmicroscopy (EM) [5, 6]. Recent
research involving AFM combined with reconstitution experiments
has shown that the efficiency of the chromatin reconstitution by
the salt dialysis method is drastically increased simply by using
longer (>100 kb) and supercoiled DNA [7, 8]. This suggests that the
physical properties of DNA are critical for higher-order chromatin
folding. AFM analyses have also revealed similarities and differences
between eukaryotic and prokaryotic genome organizations. The
fundamental structural units are very different due to the presence
of different structural proteins in eukarya, bacteria, and archaea;
that is, nucleosomes in eukarya and some archaea and non-
nucleosome units in bacteria and other archaea. Nevertheless, the
higher-order stepwise hierarchies are shared among these three
domains of life. In this chapter we shall highlight the usefulness of
AFM to studies on genome-folding mechanisms by focusing on the
similarities and differences among the three domains of life.
