Laboratory for Biomolecular Interactions and Spectroscopy

Laboratory for Biomolecular Interactions and Spectroscopy

 

Research objectives

Targeted properties of small molecules:

Design and synthesis of new small molecules that non-covalently bind to DNA / RNA, determination of their affinity and mode of binding as well as DNA/RNA induced spectroscopic changes.

Recognition is manifested by difference in affinity and / or differences in spectroscopic response caused by binding of small molecule to targeted DNA / RNA.

Small molecules designed and synthesized are characterized by heterocyclic aromatic systems (usually DNA / RNA intercalators, such as pyrene, phenanthridine, etc.) equipped by various substituents that control selectivity.

Applicability of expertise in studies of non-covalent interactions of small molecules with biomacromolecules: 

Increasing number and complexity of methods which are applied for studies of interactions of small molecules with biologically important macromolecules mostly exceed research capabilities of a single scientist. Therefore, for an efficient research in this area research teams are essential, preferentially consisting of scientists with different education background (chemists, biologists, etc). A large number of research groups in Croatia as well as in the EU occasionally or continuously have a need to examine the interaction of their small molecules with biomacromolecules at the simplest level (small molecule + biomacromolecule in biologically relevant medium). Consequently, in the last 10 years group has published joined research results with 12 research groups.

Multidisciplinary research line:

Research of LBIS group is closely coordinated with groups that study in vitrobiological activity of small molecules based on direct or indirect damage cellular DNA or RNA within the Croatian National Program No 0982914 as well as through the formal collaboration on the Ruđer Bošković Institute (Dr. sc. M. Kralj, Division of Molecular Medicine). It should be stressed that results (information about small molecule-DNA/RNA interactions at the simplest level), more often than not save time and valuable material needed for biological testing and moreover frequently influence the choice of biological methods for study of detailed mechanisms of action. 

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Biserka Žinić
Dr. Sc.

Senior research associate, Associate Professor
+385 1 456 1066
1466
385 99 3093322

Dijana Saftić
PhD

Senior research assistant
+385 1 456 1066
1466

Ivo Crnolatac
dr.sc.

Senior assistant
+385 1 457 1326
1537

Ivo Piantanida
dr. sc.

senior scientist
+385 1 457 1326
1537

Lidija-Marija Tumir
dr. sc.

Research associate
+385 1 457 1220
1775

Marijana Radić Stojković
dr.sc.

Research associate
+385 1 457 1220
1775

Renata Kobetić
dr.sc.

research assistant
+385 1 457 1220
1775 1523

B) HAMAG-BICRO Proof of concept programme: PoC6_11_47 "New diagnostic method for Alzheimer type dementia"

Glavni istraživač / voditelj: Ivo Crnolatac

With this project we aim to check the validity of the new diagnostic method for Alzheimer type dementia. The members of the project team are experts in molecular neuropsychiatry, biomolecular interactions and protein chemistry. The partners on the project are the leading Croatian specialists for Alzheimer type dementia. 

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C) ESF - HR.3.2.01-0254 "Enhacement of the capacity in medicinal chemistry and bioactive systems research".

Glavni istraživač / voditelj: Ivo Piantanida

RBI Project team of five young researchers and postdocs works on scientific research in medicinal chemistry, relevant for the Croatian pharmaceutical industry and Health sector. The enhacement of the leadership, entrapreneurship and research capabilities of young researchers and postdocs will be fullfiled by education on specific workshops. With the aim of establishing connection with the scientists in the European research area, the dissemination of the project results will be accomplished.

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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

Glavni istraživač / voditelj: Ivo Piantanida

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.

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E) Innomol: New Molecular Solutions in Research and Development for Innovative Drugs

E) Innomol: New Molecular Solutions in Research and Development for Innovative Drugs

The largest infrastructure project with the highest budget in natural sciences ever to be conducted in Croatia will foster a research pipeline at the RBI and facilitate innovation and technology for the investigation of relevant diseases such as cancer.

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F) Design, synthesis and research of interactions of small molecules with DNA, RNA and proteins

Glavni istraživač / voditelj: Ivo Piantanida

The project funded by Ministry of Science, education and sports, "Design, synthesis and research of interactions of small molecules with DNA, RNA and proteins" No. 098-0982914-2918 (PI: Ivo Piantanida)

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H) Croatian-Slovenian bilateral project

Glavni istraživač / voditelj: Ivo Piantanida

2012 – 2013:Croatian-Slovenian bilateral project with Prof. Jurij Lah, Univerza v Ljubljani, Fakulteta za kemijo in kemijsko tehnologijo, Slovenija

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J) Croatian-German bilateral project

Glavni istraživač / voditelj: Ivo Piantanida

2012 – 2013: Croatian-German bilateral project with Prof. Frank Würthner, Julius-Maximilians-Universität Würzburg, Germany

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CD-ORD spectrometer Jasco J-815

Circular Dichroism and Optical Rotational Dispersion Spectrometer (CD-ORD)

Spectrometer Jasco J-815 measures spectra of circular dichroism CD and optical rotational dichroism ORD, together with simultaneous measurement of several variants of UV/vis spectra.
During the measurement instrument is under flow of nitrogen.

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Agilent Eclipse with the temperature control

Fluorescence spectrophotometer Agilent Eclipse

Fluorescence spectrophotometer Agilent Eclipse

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IR Spectrometer

IR Spectrometer

Fourier Transform Infrared (FTIR) spektrometar ABB Bomem MB102 can be used to record IR spectra of solid and liquid samples in transmission and reflexion mode as well as at different temperatures in the spectral range 4000 – 200 cm-1.

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Microcalorimetry

Microcalorimetry

MicroCal VP-ITC;

TA Instruments DSC

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Microviscometry

Microviscometry

Lovis 2000 M is a rolling-ball viscometer which measures the rolling time of a ball through transparent and opaque liquids according to Hoeppler's falling ball principle

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UV/vis spektrometar Varian Cari 100 Bio

Ultraviolet / visual spectrometer

UV / vis spectrometer Varian Cary 100 Bio records spectra in double beam and single beam mode.
Spectral range: 190 - 900 nm

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Highlights of the recent research results

The examples of the recognition of the specificities of secondary structures various DNA/RNA using small molecules and the recognition of the nucleobase or sequences of nucleobases as a part of the DNA/RNA molecule.

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Selected references 2011 - 2016:

 

J. Matić, F. Šupljika, N. Tir , P. Piotrowski, C. Schmuck, M. Abramić, I. Piantanida*, S. Tomić “Guanidiniocarbonyl-pyrrole -aryl conjugates as inhibitors of human dipeptidyl peptidase III: combined experimental and computational study”RSC Advances, 6, 2016, 83044 – 83052

I. Crnolatac, I. Rogan, B. Majić, S. Tomić, T. Deligeorgiev, G. Horvat, D. Makuc, J. Plavec, G. Pescitelli, I Piantanida* “Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response”Anal. Chim. Acta(2016) accepted

A. Smolko, F. Šupljika, J. Martinčić, N. Jajčanin-Jozić, M. Grabar-Branilović, S. Tomić, J. Ludwig-Müller, I. Piantanida*, B. Salopek-Sondi „The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: the Cys139 is crucial for the enzyme activity and the Cys320 regulates enzyme stability“Chem. Phys. Phys. Chem. 18 (2016) 8890-8900.

Gershberg, Jana; Radić Stojković, Marijana; Škugor, Marko; Tomić, Sanja; Rehm, Thomas H.; Rehm, Stephanie; Saha-Möller, Chantu R.; Piantanida, Ivo; Würthner, Frank. Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes. // Chemistry - A European Journal. 21 (2015) , 21; 7886-7895

Svečnjak,Lidija;Baranović,Goran;Vinceković,Marko;Prđun,Saša;Bubalo,Dragan;TlakGajger,Ivana.An Approach for Routine Analytical Detection Of Beeswax Adulteration Using FTIR-ATR Spectroscopy, J. Apicult. Sci.59(2)(2015) 37-49.DOI: 10.1515/JAS‑2015-0018.

J. González-García, S. Tomić, A. Lopera, L. Guijarro, I. Piantanida,* E. García-España; “Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by a combination of aromatic, hydrogen bond and electrostatic interactions”,Org. Biomol. Chem., 13, (2015), 1732–1740.

Šegota,Suzana;Vojta,Danijela;Kendziora,Dania;Ahmed,Ishtiaq;Fruk,Ljiljana;Baranović,Goran.Ligand-Dependent Nanoparticle Clustering within Lipid Membranes Induced by Surrounding Medium,J. Phys. Chem. B119(2015)5208–5219.DOI: 10.1021/acs.jpcb.5b00898.

Svečnjak, Lidija; Bubalo, Dragan;Baranović, Goran; Novosel, Hrvoje. Optimization of FTIR-ATR spectroscopy for botanical authentication of unifloral honey types and melissopalynological data prediction,Eur. Food Res. Technol.240(2015) 1101-1115. DOI 10.1007/s00217-015-2414-1.

Šegota,Suzana;Vojta,Danijela;Pletikapić,Galja;Baranović,Goran.Ionic strength and composition govern the elasticity of biological membranes. A study of model DMPC bilayers by force and transmission IR spectroscopy,Chem.Phys. Lipids,186(2015) 17–29.

Saftić, Dijana; Vianello, Robert; Žinić, Biserka. 5-Triazolyluracils and Their N1-Sulfonyl Derivatives: Intriguing Reactivity Differences in the Sulfonation of Triazole N1'-Substituted and N1'-Unsubstituted Uracil Molecules. // European journal of organic chemistry. 35 (2015) ; 7695-7704 (journal article).

Zimmermann, Boris; Baranović, Goran; Gembarovski, Dubravka. Experimental and theoretical study of the cation binding properties of macrocyclic dehydrodibenzopyrido[15]annulenes, Spectrochim. Acta Part A. 137(2015) 730-739.

Klepac, Damir; Ščetar, Mario; Baranović, Goran; Galić, Kata; Valić, Srećko. Influence of high doses γ-irradiation on oxygen permeability of linear low-density polyethylene and cast polypropylene films, Radiation Phys. Chem.97(2014) 304-312.

L.-M. Tumir, I. Crnolatac, T. Deligeorgiev, A. Vasilev, S. Kaloyanova, M. Grabar Branilović, S. Tomić, I. Piantanida, Chem., Eur. J., 18 (2012), 3859–3864

L.-M. Tumir, M. Radić Stojković, I. Piantanida*; “Come-back of phenanthridine and phenanthridinium derivatives in 21st century”,Beilstein J. Org. Chem.10, (2014), 2930–2954.

J. Wu, Y. Zou, W. Sicking, I. Piantanida, T. Yi, C. Schmuck,J. Am. Chem. Soc. , 134 (2012), 1958–1961.

K. Klemm, M. Radić Stojković, G. Horvat, V. Tomišić, I. Piantanida, C. Schmuck;Chem., Eur. J., 18 (2012) 1352–1363.

M. Radić Stojković, S. Miljanić, K. Mišković, Lj. Glavaš-Obrovac, I. Piantanida;Mol. BioSyst., 7 (2011) 1753–1765.