Lay summary
This NF-grant application contains four separate sub-projects that all deal with the design, synthesis and the evaluation of novel, chemically modified oligonucleotide analogues. These analogues are of interest for DNA therapy, for DNA based diagnostics, as molecular architectures for DNA based functional materials or as tools to follow cellular metabolism. The first sub-project deals with the synthesis of novel nucleosides and oligonucleotides of the bicyclo-DNA family with the aim of improving RNA affinity and cellular uptake and distribution. Molecular modeling has been used as a designer tool to improve RNA affinity. The pro-drug concept has been applied to enhance membrane permeability. The second sub-project is devoted to the optimization of our recently discovered phenanthrene DNA-zipper recognition motif. Also here, molecular dynamics on a QM/MM level will be used for identifying the best geometries of differently attached phenanthrene units in the base stack and for predicting the ionization potentials of differently substituted phenanthrene units. Further experiments are devoted to the structural characterization of multiply substituted duplexes by X-ray crystallography and to the investigation of the charge transport properties through the phenanthrene units by using nanoelectrochemical methods. The ultimate goal here is to construct an efficient charge separating device based on this novel DNA architecture. Another sub-project is concerned with the biological impact of damaged RNA. Having in hand a powerful method for the synthesis of abasic RNA we want now to investigate the fate of such RNA lesions during translation at the ribosome. In addition we will synthesize RNA with the oxidatively damaged bases 5-hydroxyuracil and 5-hydroxycytosine and investigate their impact on transcription and translation. The results of this sub-project will increase our general understanding of the biological impact of such RNA lesions that can occur naturally. The final sub-project aims at improving the selectivity and sensitivity of current RNA or DNA detection systems by using hybrid DNA/homo-DNA probes. This system is based on a homo-DNA templated Staudinger reaction, converting a covalently attached non-fluorescent to a fluorescent dye upon RNA target recognition. This system is designed towards catalytic signal enhancement and should thus lead to high sensitivity probes allowing the detection of low abundance RNA probes. In addition the use of a bioorthogonal base-pairing system (homo-DNA) and a bioorthogonal chemical reaction (Staudinger reaction) is expected to lead to less false positive signals and may show improved in vivo performance.