The present invention provides a method for analysing the interaction of one or more nucleotide sequence(s) from one or more region(s) of interest with other nucleotides sequences in a three-dimensional DNA structure, comprising the steps of: (a) providing a sample of crosslinked DNA; (b) digesting the cross-linked DNA with a first restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross-linking; e) fragmenting the ligation and ligated molecules from (d); (f) hybridising the fragments from (e) to one or more oligonucleotides representing the sequences which are adjacent to the cleavage site of the first restriction enzyme in order to enrich for the ends of the nucleotide sequences that have been ligated to another nucleotide sequence in step (c); and (g) analysing the nucleotide sequence of the enriched fragments in order to identify the nucleotide sequences involved in interaction(s).