Investigation of the hybridization process in DNA-microarrays by fluorescence lifetime imaging

cDNA-microarrays for expression profiling rely on the assumption that the fluorescence signal is linearly proportional to the concentration of the markers. Yet, interactions amongst different markers and with the substrate might affect the chromophore quantum yield and lead to an erroneous reading. To indirectly evaluate quantum yield changes and their relevance for DNA-microarray reading, we studied the effect on fluorescence lifetime by using a system for fluorescence lifetime imaging. Quenching of the fluorescence emission was observed in the tight environment represented by a DNA-n-microarray due to concentration and to interactions with the processing chemicals present on the substrate.