Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin.

The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuation of ligand interaction the enzyme cuts along regions containing dG-dC pairs sandwiched between dA-dT pairs. This follows a slow kinetics and is associated with a release of netropsin from those segments. These facts suggests the usefulness of the partial protection of certain DNA sequences in DNAase I cleavage sites in producing DNA fragments in structural studies of the genome. A possible interpretation of the effect of netropsin binding on the enzymatic hydrolysis of phosphodiester bonds of the helix is discussed.