Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 200: Poster Session II

AKB 200.60: Poster

Tuesday, March 8, 2005, 17:00–19:00, Poster TU C

Potential and limitations of DNA microarrays from a single-molecule point of view — •Beate Sick and Keith Harshman — DNA Array Facility, Universitaet Lausanne, CH-1015 Lausanne

DNA microarrays are a high-throughput technology which provide a snapshot of the transcriptome of some ten thousand genes in parallel. Since the native RNA expression levels in a cell can span a range of 6 orders of magnitude, it is desirable to cover the same dynamic range in one microarray experiment. In order to approach this goal several components in a microarray experiment have still to be optimized. In this contribution we assess physical limitations of DNA microarray experiments and include technical boundaries and biological variability. We discuss the observed limited reproducibility and dynamic range of typical microarray data from homemade spotted arrays and from commercial platforms (Affymetrix). The ultimate lower detection limit is reached when a single target gene transcript binds to a probe feature, provided the instrumentation has single-molecule sensitivity. On the other hand, the total number of binding sites for transcripts on each feature, which is determined for instance by the feature size, defines the ultimate upper detection limit. From these theoretical considerations the accessible dynamic range is evaluated for different existing platforms. In an outlook the impact of further miniaturization of microarrays on the dynamic range will be discussed.