A simple probe for DNA accessibility in chromatin

When DNA is treated with Cu(II) and then heated, the melting temperature (Tm) of the DNA is dramatically decreased (8). The Cu(II) binds to the DNA in such a way as to destabilize the double helix and help to break the hydrogen bonds between the bases. When soluble chromatin is similarly treated with Cu(II) and heated, the Tm is unaffected. Apparently the Cu(II) cannot penetrate the chromatin structure and thus cannot initiate the DNA destabilization process. However, when H-1 histone is removed from the chromatin by affinity chromatography, subsequent treatment with Cu(II) does lead to a lowered Tm when the chromatin is heated. This Tm lowering is also achieved by two less drastic techniques that do not remove histone H-1, but decrease the affinity of the H-1 to the DNA: (1) a mild acetylation procedure that specifically modifies either 2 or 4 epsilon-amino groups of lysines on the H-1 histone, and (2) reaction with phosphate-binding divalent metal ions, e.g., Mg(II), Mn(II), or Co(II). Apparently, removal of H-1 or decreased affinity of H-1 for DNA increases the accessibility of the DNA to the Cu(II). This phenomenon suggests a very simple qualitative probe for the degree of structural change in chromatin produced by a change in the stability of the DNA-H-1 interaction.