Figure 6

Alternative scenarios for probe-target binding configurations. a. a configuration where the duplex is fully-formed. A mismatch might cause some loss of hydrogen bonding at the mismatch position, and possibly at a small number of adjacent base pairs, indicated by the loop. If all of the probes were in this type of configuration, mismatch position would not be expected to have any significant effect. b. a configuration where the duplex is partially formed. A mismatch that occurs in a region where the duplex is not formed has no effect on the stability of the hybrid. This is more likely for mismatches near the ends of the probe. c. the same configuration as 6b, but in this case the mismatch is near the centre of the probe, and so lies within the duplex region and will have some effect on the stability of the hybrid (this might be the loss of a few hydrogen bonds, as in figure 6a, a total disruption of the duplex or some intermediate scenario). These figures are intended as schematic diagrams of some possible duplex configurations, not as detailed representations of any particular duplex.