Molecular recognition of nucleic acids is of fundamental importance e.g. for gene transcription and regulation, protein synthesis or cell-division. Small molecules selectively targeting specific DNAs or RNAs are therefore highly interesting not only to understand such processes in more detail on a molecular level but also for potential medicinal applications, as sensors or probes for fluorescence based bioimaging as well as for analytical purposes in isolated biosamples.
In this project we want to design, synthesize and study highly selective probes for the sensing of nucleic acid secondary structures with special emphasis on the multi-purpose probes: single molecules able to simultaneously differentiate by several highly sensitive spectrometric methods between the most common secondary structures of ds- DNA/RNA. To develop compounds with increased affinity and selectivity and more pronounced fluorimetric responses, we plan to test new, more efficient fluorophores (cyanine, phenanthridine, fluorescent nucleobase derivatives - Piantanida group) combined with pyrrole-guanidinium cations (partner from Duisburg-Essen University; Schmuck group) and explore structural diversity of the compounds, using a combinatorial approach based on peptide backbone carrying recognition units prepared by solid phase synthesis. The interaction with DNA/RNA will be studied by Piantanida group (UV/Vis, fluorescence, CD/LD spectroscopy, viscometry and DSC/ITC microcalorimetry, MS, NMR, X-ray, CLSM), while expertise not available in Croatia (pyrrole-guanidinium coupling, oligopeptide libraries screening) will be performed in collaboration with Schmuck group.
This project is based on the very efficient collaboration between the working groups of Dr. Ivo Piantanida (Ruđer Bošković Institute, Zagreb, Croatia) and Prof. Dr. Carsten Schmuck (Universität Duisburg-Essen, Germany), which started in 2007 within FP7 COST Action D31. The initial aim was to develop new chemical receptors for the molecular recognition of nucleic acids, which can be used e.g. as sensors to differentiate between different types of nucleic acids (DNA versus RNA) or different nucleic acid sequences. Currently the focus is shifting towards the recognition of nucleic acid secondary structure, for example the sensing of different size and shape of the grooves, respectively; as well as to the broad spectrum of biochemical applications.
Moreover, previous Piantanida-Schmuck collaboration is significantly fostered by joining of the nucleoside chemistry group (dr. B. Žinić et al) to this project, who will contribute to the project by synthesis and characterisation of novel nucleobase-amino acids and PNA oligomers. Furthermore, new team members are NMR expert (dr. V. Smrečki), crystallography expert (dr. A. Višnjevac) and mass spectrometry expert (dr. R. Kobetić), who will contribute to the better structural understanding of studied small molecule – DNA/RNA complexes.