in the duplex formed by hybridization of the target to the capture moiety for example the duplex binding ligand actinomycin d binds preferentially to the sequence 5 39 agct 3 39 illustratively the capture moiety may be chosen to have the 5 39 terminal sequence 5 39 ct as part of an intramolecular duplex and the target strand is selected or modified to have the 3 39 terminal sequence ag 3 39 thus upon hybridization of the target strand to the capture moiety the nicked duplex 5 39 ag ct 3 39 is formed wherein the 34 g c 34 represents the nick between g and c this embodiment is particularly useful when discrimination between target sequences of differing length e g cut and uncut targets are used if the longer target sequence forms an overhang when hybridized to the hairpin capture moiety addition of a duplex binding ligand which has a recognition site which includes the nick site will improve discrimination between cut and uncut target sequences as described in more detail below and in examples 1 and 2 the capture moiety can also be selected so that a duplex binding ligand binding site will form in a region which does not include an intramolecular duplex e g the duplex binding ligand binding site does not include a nick in preferred embodiments the.