Figure 1

Fluorescence micrograph (taken with an Olympus IX81 epi-fluorescence microscope and a Hamamatsu EM-CCD camera) of a microarray feature-block comprising variations of the 16 mer probe sequence motif 3'-TATTACTGGACCTGAC-5'. Microarray hybridization was performed with the 5'-Cy3-labeled RNA oligonucleotide target 3'-AACUCGCUAUAAUGACCUGGACUG-5' (target concentration: 1 nM in 5 × SSPE, pH 7.4, 0.01% Tween-20, T = 30°C). Each 3 × 3 sub-array comprises (randomly arranged) one perfect matching probe, three single base mismatch probes, four insertion probes and one single base deletion probe. In Fig. 2A the hybridization signals (fluorescence intensities, averaged over the center of the microarray features) are plotted versus the defect position. The size of each microarray feature is 21 μm and the pitch of the array is 35 μm. The significantly brighter feature-block at left comprises variations of the 20 mer probe sequence motif 3'-TTGAGCGATATTACTGGACC-5'.