Dresden 2006 – scientific programme

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AKB: Biologische Physik

AKB 30: Poster Session I

AKB 30.31: Poster

Monday, March 27, 2006, 15:30–18:00, P1

Hybridization and melting experiments on oligonucleotide microarrays — •Thomas Naiser and Albrecht Ott — Physikalisches Institut, Universität Bayreuth, 95440 Bayreuth

DNA microarrays are becoming an increasingly important tool for the quantitative determination of gene expression levels. We use a light-directed in situ synthesis process, employing a ’programmable mask’ based photolithography technique, to produce short oligonucleotide microarrays, comprising a multitude of different features. Each feature contains a large number of surface bound probe molecules of the same, given sequence. We apply the fluorescently labeled target strands to the microarray surface in a buffer solution. Driven by diffusion, these strands can freely move over the microarray surface to make contact with a large number of different probe molecules. They form a relatively stable duplex with complementary sequence probe molecules. The fluorescence intensity of these hybridized targets provides an estimate for the abundance of a particular target nucleic acid. In hybridization and melting experiments we study how sequence mismatches between probe and target molecules affect hybridization efficiency. Secondary structure of the targets (caused by intramolecular base pairing) is supposed to affect the accessibility of the sequence ranges targeted by the probes.We investigate the effects of target secondary structure on probe sensitivity by probing long cRNA targets with sets of all 25mer probe sequences, which are complementary to the particular cRNA target.