Figure 6.

Stability orders of 12 single-base mismatch types for hybridization in solution (b) and on microarrays (a, c, d, e). For a hybridization oligonucleotides duplex X/Y, X refers to probe and Y refers to target. For example, the microarray hybridization in our study is DNA/RNA, which means the probe is DNA and the target is RNA - cRNA used by an Affymetrix experiment. We refer to Naiser et al. (2008) for details. Specifically, both Wick et al (2006) and our study used log₂(PM/MM) as the measure of discriminating ability, which has an opposite order compared to stability. Thus, the larger log₂(PM/MM) value corresponds to the lower stability of duplex. Please note that there are two notations used under each study: the upper one is the notation that is commonly used- for consistency to that in Naiser et al (2008); the lower one is the notation indicating the base change from a perfect matched probe to a mismatched probe - primarily used in the current study. For example, C U in the common notation means the probe provides C and the target provides U for the mismatched base pair, while in the second notation it's A C indicating A is the base on the perfect matched probe and changes to C on the mismatched probe.