Single stranded DNA is an often unattended by-product of a PCR and also an ingredient of every hybridization approach which contains PCR-products. Total ssDNA comprises of abortion products, which are generated when the polymerase dissociates from its template during Diperodon elongation, and full-length products. Single stranded full-length products may exist only of one type of strand at a time because two complementary strands would hybridize with each other. Therefore, only the excess strand is available as ssDNA and can hybridize directly to its corresponding probe. We developed a new model for the hybridization mechanism which relies on the principle that dsDNA is almost unable to bind to capture probes without ssDNA as catalyst. A possible mechanism of ssDNA induced probe hybridization would be that at first the excess strand hybridizes to its probe. The resulting dangling ends could again act as probes as described earlier. These single stranded dangling ends would have two advantages in binding to double stranded PCR-products compared to covalently bound oligonucleotide probes. On the one hand, they are generally much longer, resulting in a more stable hybridization. On the other hand, their terminal sequence matches the sequence of the end of the PCR-product. Denaturing of a few bases is much more likely to occur at the end of a double stranded PCR-product than in the middle of it. This could enable the dangling tail to attack this end and partially hybridize to its complementary strand. Via a branch migration mechanism the former dangling end could displace the other strand. A complete release of this strand 
would regenerate the original free ssDNA enabling further reaction cycles. According to the mentioned mechanisms, the displacement of probe bound dsDNA is also possible, so that dissolved and attached dsDNA are in steady state equilibrium after some time. The proposed mechanism shown in Figure 9 is theoretically, and several similar reaction mechanisms are imaginable, such as a further branching of the strand agglomerate shown in Figure 9 C forming branched DNA, as observed recently. Aggregates of multiple sense and antisense strands bound to capture probes have been described already. A beneficial effect of increased ssDNA generation on microarray signals, for example by asymmetric PCR, has already been described, too, but the mechanism of action has not been characterized, yet. Another method already in use to increase the ssDNA content in the hybridization mixture is to initially separate the strands of the PCR-product by heat denaturation. However, the amount of ssDNA declines over time due to renaturation of both strands. Our experiments indicate that ssDNA strongly enhances the hybridization of PCR-products to the probe configuration specific for the ssDNA. The increased generation of one specific strand in an asymmetric PCR and the addition of synthetic ssDNA, respectively, had led to drastic changes of the s/as-ratio of some probes. According to our model, the addition of synthetic sense ssDNA increased the signal of antisense probes by providing a catalyst for the hybridization and decreased the signal of the sense probe in return by reducing the amount of free antisense strand. The considerable extent of the signal shift supports the assumption that ssDNA is essential for efficient hybridization. In an equimolar PCR, a signal shift of some probes could be observed, too, when the overall primer Amikacin hydrate concentration in the PCR was reduced.