Figure 4.

The hybridization performance of long oligonucleotides in relation to internal versus terminal mismatches. Ten putative genes were chosen arbitrarily. Each gene is represented by a series of ten oligonucleotides. The first (rightmost) oligonucleotide in each series represents a perfect match to the target sequence. Mismatches were introduced in increasing numbers (10% steps) into each subsequent oligonucleotide in each series. The pattern of matches and mismatches within each oligonucleotide is shown below each graph, where a black bar indicates a perfect match and a gray bar indicates a mismatch. (a-e) Mismatch positions were randomized ('distributed set'). (g-k) Mismatch positions were chosen such that a contiguous stretch of perfect-match sequence remained in the middle of the oligonucleotide ('anchored set'). The average hybridization performance, measured as the normalized total intensity for 16 independent experiments, is plotted for each oligonucleotide. (f) The average plot for a-e; (l) the average plot for g-k.