Harnessing the writhe: a role for DNA chaperones in nucleoprotein-complex formation

In both the eukaryotic nucleus and the prokaryotic nucleoid, much of the DNA is organized into complex nucleoprotein assemblies in which DNA is compacted by looping or by wrapping on a protein surface. Some assemblies are required for the processes of initiation of transcription, DNA replication and site-specific recombination, while others, such as the nucleosome, package and organize DNA. The DNA in these assemblies is both highly ordered and deformed. For example, in the nucleosome core particle, 145 base pairs of DNA are wrapped in 1.8 left-handed superhelical turns, equivalent to a bend of 47 degree for each double-helical turn. Yet in solution, DNA molecules are too rigid to achieve this degree of folding in the absence of interacting proteins. This implies that the assembly of such structures must surmount a significant energetic barrier. One way to overcome this penalty would be to maintain the DNA in an appropriate configuration before complex formation.