Selectivity in the interaction of various DNA sequences with H1 histone.

An assay for the binding of H1 histone by DNA was developed based on extraction with phenol, which partitions free DNA into the aqueous layer and aggregates of H1 histone-DNA complexes into the phenol layer and interface. When this assay was performed on fragments of simian virus 40 (SV40) DNA, fragments containing the 21-bp repetitive element and a portion of the origin of replication were resistant to H1 binding. This result was corroborated when an endonuclease protection assay showed that the origin was poorly protected by H1 compared to other sites. DNase I protection mapping demonstrated that H1 "underprotected" sites immediately to either side of the AT element, which lies in the origin of replication. These sites were also hypersensitive to attack by hydroxyl radical in the absence of histone, probably indicative of some conformation aberration such as minor-groove distension. The same DNA sequences resistant to binding H1 histone resisted binding to H4 histone but showed much less selectivity, if any, in binding polylysine. These results clearly demonstrate that the interaction of DNA and H1 (and H4 histone) is more complicated than just charge neutralization and probably involves the conformation of the DNA.