DNA-bridging by a palindromic alpha-helix.

The nucleosomal DNA repeat of 240 base pairs in the chromatin structure of sea urchin sperm is exceptionally long and is accompanied by the presence of a histone H1 molecule larger than is usual in most species of chromatin. I propose how these two features are correlated and how they fit into the solenoidal model for the 300-A-diameter fiber of chromatin. Comparison of the sequence of spermatogenous H1 with other H1 sequences reveals an insert of 55 amino acid residues (residues 122-176). A 37-residue sequence in the insert (residues 140-176) has a palindromic character. I propose that each half of the palindromic sequence constitutes an alpha-helical DNA-binding unit and that the continuous alpha-helix made up of the two halves, by virtue of its palindromic nature, stabilizes the formation of an extra superhelical turn by the long linker DNA between two nucleosome cores. The N-terminal-C-terminal "polarity" of each alpha-helical section of half the palindromic sequence indicates how the arginine/lysine-rich DNA-binding surface of the alpha-helical section is used. The polarity of the H1 insertion sequence supports the so-called "reverse-loop" model or a "figure-eight" model for the path of the DNA within the solenoid structure; i.e., the linker DNA forms a right-handed superhelical turn toward the center of the solenoid structure. This use of a pair of a palindromically related alpha-helical sections has a similarity with the "scissors-grip" model for the interaction of the leucine-zipper proteins with DNA.