Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 28: Molecular Recognition
BP 28.3: Talk
Friday, February 29, 2008, 11:15–11:30, PC 203
The impact of defects on the binding affinity of surface bound oligonucleotide-duplexes — Thomas Naiser1, Oliver Ehler1, •Jona Kayser1, Timo Mai1, Wolfgang Michel1, and Albrecht Ott1,2 — 1Experimentalphysik I, Universität Bayreuth, D-95440 Bayreuth, Germany — 2Biologische Experimentalphysik, Universität des Saarlandes, D-66041 Saarbrücken, Germany
It is not fully understood how point defects and loop insertion affect the stability of DNA duplexes. This is for example of interest in the context of genotyping microarrays which base on the reduced binding affinity of non-perfect match duplexes. In order to study the complex problem of surface based hybridization in more detail, we performed array based hybridization experiments in simple and well controlled situations without competitive binding. The microarrays are produced in our lab using Light Directed Polymerization (LDP) of phosphoramedites on a dendrimer substrate. This technique provides a high flexibility in array design. We report a strong positional dependence of the influence of single base bulges and single base mismatches with increasing importance towards the middle of the strand. To explain the observed behavior we propose a molecular zipper. Direct comparison between binding affinities of DNA/DNA and RNA/DNA duplexes shows that for RNA/DNA purine-purine mismatches are most destabilizing whereas for DNA/DNA the affected base pair is the relevant parameter. We attribute these differences to the different structures of the duplexes (A vs. B form).