D) Multifunctional molecular sensing of DNA/RNA secondary structure by chemical sensors - DNA/RNA-MolSense

D) Multifunctional molecular sensing of DNA/RNA secondary structure by chemical sensors - DNA/RNA-MolSense
Datum početka projekta
Datum kraja projekta
Kategorija projekta
Projekti Hrvatske zaklade za znanost
Ugovoreni iznos financiranja
988.000,00 HRK
Šifra projekta
HrZZ projekt broj 1477

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.

Glavni istraživač / voditelj
Ivo Piantanida

Ivo Piantanida, dr. sc.

znanstveni savjetnik +385 1 457 1326

Biserka Žinić

Biserka Žinić, Prof. dr. sc.

znanstveni savjetnik +385 1 456 1066
099 309 3322

Dijana Saftić

Dijana Saftić, dr. sc.

Poslijedoktorand, Viši asistent +385 1 456 1066

Renata Kobetić

Renata Kobetić, dr. sc.

znanstveni suradnik +385 1 457 1220

Željka Ban, dr.sc.

viša asistentica +385 1 456 1066

Lidija-Marija Tumir

Lidija-Marija Tumir, dr. sc.

Znanstvena suradnica +385 1 457 1220

Marijana Radić Stojković

Marijana Radić Stojković, dr.sc.

Viši znanstveni suradnik +385 1 457 1220

Ivo Crnolatac

Ivo Crnolatac, dr. sc.

znanstveni suradnik +385 1 457 1326

Aleksandar Višnjevac

Aleksandar Višnjevac, dr. sc.

viši znanstveni suradnik +385 1 457 1203

Vilko Smrečki

Vilko Smrečki, dr. sc.

viši znanstveni suradnik +385 1 456 0944

Ostali suradnici

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.

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