A number of complexes formed between peptide nucleic (PNA) acid and double-stranded (ds) DNA has been described. Each of these complexes involves different structural elements and they consequently exhibit distinct physico-chemical characteristics. Thus, it is important to know in detail with which type of complex one is dealing. To this end, the different techniques described below have proven extremely useful and the rules governing formation of certain types of complexes are, if not fully, then at least partially resolved. In contrast, the mechanism(s) by which peptide nucleic acid (PNA) binds double-stranded DNA has been much more difficult to approach. As for any mechanistic study, the main difficulty is to catch intermediates along the binding pathway, especially those of labile transition-state intermediates. Here we describe (1) the currently known PNA-dsDNA complexes, (2) the probing methods commonly employed for their analysis, and (3) protocols used in our laboratory.