Sensitivity to mismatches as demonstrated by two-color hybridization. An array was synthesized containing reporters complementary to targets 5'-Cy3-GAC CTC CCG CTC ACG CAC CT (green) and 5'-Bodipy-GAC CTC CCG GAC ACG CAC CT (red), using standard conditions described in Materials and methods. The bases in bold are different in the two reporter:target molecules. The slide was hybridized with an equimolar mixture of the two labeled target oligonucleotides and the fluorescence intensity determined on the ScanArray 5000 using the Dapple spot-finding program. The green/red ratios of the green- and red-complementary features were 3.12 ± 0.57 (N = 230) and 0.25 ± 0.05 (N = 660), respectively. Graphing Cy3 intensity vs Bodipy intensity shows excellent separation between signals and the insert shows that the effects of two base changes are clearly distinguishable by eye.
Lausted et al. Genome Biology 2004 5:R58 doi:10.1186/gb-2004-5-8-r58