Figure 2

The "defect profile" shows the position-dependent impact of single base mismatches, insertions and deletions on hybridization affinity. Symbols: MM probes with substituent bases A (red crosses), C (green circles), G (blue stars), T (light blue triangles); moving average of all MM intensities (black dashed curve); single base insertion probes with insertion bases A (red dash-dotted curve), C (green solid curve), G (blue dotted curve), T (light blue dashed curve). Defect profiles of different probe sequence motifs. (A) Position dependent impact of various single base defects on the hybridization affinity for the probe sequence motif 3'-TATTACTGGACCTGAC-5' (hybridized with the complementary RNA target sequence). Hybridization signals of single base deletions (orange dashed curve) are comparable to that of MMs at the same position. PM probe signal replicates (black symbols on gray ground) serve as an indicator for spatial bias on the microarray. Deviations of MM hybridization signals from the mean profile are mostly MM-type specific. Increased hybridization signals of certain insertion probes (where the bulged surplus base is located next to identical bases – Group II bulges [14, 53]) are due to positional degeneracy of the bulge defects. (B) Position dependent impact of various single base insertion defects on the hybridization affinity for the probe sequence motif 3'-GTTTGAATCTCACGTCGTCTCCCC-5' (hybridized with the complementary DNA target sequence). Insertions of A (red crosses), C (green circles), G (blue stars), T (light blue triangles), moving average of all insertion probe intensities (black dashed curve). Systematically increased hybridization signals of Group II bulges are discussed in Additional file 1, Fig. S2.