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BP: Fachverband Biologische Physik

BP 13: DNA/RNA and Related Enzymes

BP 13.11: Talk

Wednesday, March 28, 2012, 12:30–12:45, H 1058

Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study — •Christian Trapp — Universität des Saarlandes, Biologische Experimentalphysik

The hybridization process, the formation of the DNA double-helix from single-strands of complementary sequences, is important for all living organisms. It is at the basis of many high throughput nucleic acid based technologies such as high throughput sequencing or DNA microarrays. The latter consist of surface bound ssDNA (probes), which can selectively bind to complementary strands (targets) in solution resulting in highly parallel measurements. The underlying physical mechanisms of the hybridization process are poorly understood. We have shown that the binding to DNA microarrays can be easily modeled when the length of probe and targets match [1-2]. Here we investigate the binding of longer targets to microarrays, which hybridize to the probes forming bulged loops. We systematically vary loop position and loop size and show that the result can be reproduced with simple theoretical models at thermal equilibrium, which also apply to solution-phase experiments.

[1] Naiser T, Kayser J, Mai T, Michel W, Ott A: Stability of a Surface-Bound Oligonucleotide Duplex Inferred from Molecular Dynamics: A Study of Single Nucleotide Defects Using DNA Microarrays, Phys. Rev. Lett. 2009, 102, 218301

[2] Naiser T, Kayser J, Mai T, Michel W, Ott A: Position dependent mismatch discrimination on DNA microarrays - experiment and Model, BMC Bioinformatics 2008, 9:509