A method to locate, between restriction sites, binding sites on DNA, e.g. the positions of nucleosomes on a minichromosome. The DNA protected by binding proteins is cleaved in susceptible, i.e. unprotected, regions by non-specific chemical or enzymic methods, the protecting protein is removed, and a restriction nuclease introduces reference points recognised by complementary polynucleotide probes for subsequent analysis of the sequences from the restriction sites towards the sites at which it was initially cleaved in the unprotected regions.