At present, the NucZip model is intended for equally long nt segments. Exceptions to the model found in the experimental section of this work can be illustrated by the remarkable difference in hybridization between the short perfectly matching targets of 15-22 nt (15 nt_free, 18 nt_free and 22 nt_free) and the longer 70-mer targets (74%_15 nt, 74%_18 nt and 74%_22 nt) ( Figure 3A , B and D). Several groups have analyzed the effect of short so-called dangling ends of 1-5 nt (23) (24) (25) (26) , and report that they appear to stabilize hybridization of the duplex. Doctycz et al. observed that the dangling nt closest to the duplex contributed most to the stabilizing effect (47) . The lengths of our long mismatching ends ranged from 55 to 48 nt with a 74%-nt mismatch and no matching trimers. We speculate that the destabilization seen in a duplex with two long mismatching ends, one from the probe and one from the target, compared with a duplex between a long and a short oligonucleotide, with only one long protruding oligonucleotide, is due to shearing stress on the matching nt, or to competition from intra-strand secondary structures at the separate ends.