We have compared chicken erythrocyte linker histones Hi and H5 binding to a synthetic four-way DNA junction. Each histone binds to form a single complex, with an affinity which permits competition against a large excess of linear duplex DNA. The affinity ofH5 is higher than that ofHi. The globular domain from either protein will also bind strongly, but in this case multiple binding occurs. Binding of intact Hi is inhibited by cations: Mg2+ and spermidine are very effective, Na+ much less so. This inhibition is not likely to be a general ion-competition effect, for Mg2+ is much less effective in inhibiting the binding of H1 to linear DNA. Instead, the inhibition of binding may be due to ion-dependent changes in the conformation of the four-way junction, which are known to occur under similar conditions. These results strongly suggest that the angle formed between the arms of the DNA junction could be a major determinant in the interaction of Hi with DNA crossovers.Many studies have indicated that histone H1 and its variants interact with linker DNA in chromatin and are associated in particular with the entrance and exit of the DNA to and from the nucleosomal core particle (reviewed in refs. 1 and 2). Since many electron microscopy studies indicate that the DNA crosses itself upon entering and exiting the nucleosome (e.g., ref.3), it would seem likely that DNA crossovers would provide preferential sites for H1 binding. Early evidence suggestive of this came from studies showing that H1 interacts preferentially with highly supercoiled DNA (4-6). However, the interpretation of these experiments was complicated by the fact that under high torsional stress DNA can also adopt a variety of non-B conformations, which might themselves provide preferred sites for H1 binding. In recent studies we have shown that H1 will exhibit a preference for even weakly supercoiled DNA, where such non-B structures are not formed, as compared with relaxed DNA (7). Others have suggested that four-way junction (4WJ) DNA should be structurally similar to DNA crossovers (8). 4WJ DNA is the core structure of cruciform DNA (which may extrude from palindromic sequences under torsional stress) and the Holiday junction (which forms during homologous recombination). Stable 4WJs can also be formed by annealing appropriately chosen oligonucleotides in vitro (9), and thus provide a convenient model system to study proteins which might interact specifically with this type of DNA structure.These previous results and the demonstration by Bianchi et al. (10) (14,15). It is similar in sequence and structure to H1 but has multiple lysine-to-arginine substitutions relative to H1. It is believed, but not known with certainty, that H5 occupies sites in chromatin that are similar to those taken by H1. Therefore, it seemed important to extend our studies to include this special lysine-rich histone.All linker histones share a common three-dimensional structure-there exists a folded globular region which is flanked by less structured N-and C-terminal "tail...