FIGURE 8.

Middle-base related sensitivity of probe pairs with B = A, T, G, C in the middle of the PM sequence (see the figure for assignments and Eq. 2) as a function of the concentration of specific transcripts. The concentration ranges of dominating nonspecific (NS) and of specific (S) hybridization are indicated by vertical dotted lines. The duplet in the limit of nonspecific hybridization transforms into a triplet-like pattern in the limit of specific hybridization. The sensitivity provides a measure of the base-specific contribution to the free energy of RNA/DNA duplex stability.