Three matching trimers account for approximately one turn [10.4 nt (44) ] of the helix of a dsDNA molecule. It is thus likely that two long DNA strands become entangled or conformationally committed when at least one turn of the helix has been completed. Nucleation has to proceed rapidly, without too much torsion and entanglement, to allow many encounters in a short time. We envision that contact between two strands extending to 9 nt allows rapid comparison between strands with only local torsional disturbance. If the brief contact does not achieve binding strength over a certain threshold (the nucleation threshold), the strands separate and new comparisons are made. If the nucleation threshold is exceeded at initial contact, Total ZipScore mode1 : 25+12+12=49 Total ZipScore mode2 : 25+12+5+1=43 ZipScore downstream : 49-dInosinefactor*(49-43)+(dInoCnr*dInoCfactor) contiguous tri-to pentadecamers Figure 8 . The zipping component of NucZip. When a 6-9-bp sequence fulfilling the nucleation criteria has been detected, hybridization up and downstream of the nucleating site is attempted (zipping). The figure shows the downstream zipping process, with successive accumulation of score within a matching segment arising from the trimers, tetramers, etc. up to pentadecamers (each scoring equally) which fit into it. In this way, a longer matching segment gets more than a linear increase in score relative to a shorter one. Zipping extends from the potential nucleation site, terminating with a mismatch or the end of one of the strands. dInosines are counted as intermediate between a match and a mismatch, as described in the 'Materials and Methods' section. If several consecutive matching segments are encountered, their scores are added. binding extends further up and downstream, i.e. zipping occurs. This proceeds as long as the binding strength remains sufficient. The strands are held together chemically by base-base interactions and topologically by the multiple turns of intertwinement. It was a challenge to model this process. In the NucZip model, the program first tests for possible nucleation sites and selects the two highest scoring sites for further evaluation. Zipping is then performed up and downstream from each suggested nucleation site. The zipping algorithm symbolizes the successive cooperativity of binding by adding the number of successive tri-to pentadecamers for each matching segment, each of which ends either in a mismatch or at the end of one or two of the oligonucleotides. The contribution of added dInosine molecules is counted less than those of proper matches. The highest scoring nucleation point is chosen as the result. The results using degenerated probes were in line with this NucZip theory. A long matching segment created by a wobble position increased hybridization strength beyond the contribution of the additional single match.