Berlin 2008 – scientific programme

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BP: Fachverband Biologische Physik

BP 28: Molecular Recognition

BP 28.7: Talk

Friday, February 29, 2008, 12:15–12:30, PC 203

separation of specific sequence oligonucleotides from a yeast genome using single primer abrupt termination PCR (SPAT-PCR) — •harish bokkasam — Department of Biological Experimental Physics, University of Saarbrücken, Saarbrücken, Germany

As a step towards gene expression analysis with short DNA fragments (20-50 bp), we develop a novel technique for fishing out a sequence specific oligonucleotide from a yeast genome. This method is based on SPAT-PCR, using a single primer and a temperature jump resulting in abrupt termination of the PCR cycle and interruption of the elongation of the primer on the RNA template. We design a complementary primer to select the specific sequence oligonucleotide (SSON). The intermediate product, consisting of the required SSON, excess primer and RNA template, is visualized and subsequently separated using gel-electrophoresis. The obtained SSON then serves as template for PCR amplification. The accuracy of this method can further be tested by using the obtained SSON as a target in array-based hybridisation experiments.