Analytical and Structural Studies for the Investigation of Oxidative Stress in Guanine Oligonucleotides

DNA damage plays a decisive role in epigenetic effects. The detection and analysis of DNA damages, like the most common change of guanine (G) to 8-oxo-7,8-dihydroguanine (OG), is a key factor in cancer research. It is especially true for G quadruplex structure (GQ), which is one of the best-known examples of a non-canonical DNA arrangement. In the present work, we provided an overview on analytical methods in connection with the detection of OG in oligonucleotides with GQ-forming capacity. Focusing on the last five years, novel electrochemical tools, like dedicated electrodes, were overviewed, as well as different optical methods (fluorometric assays, resonance light scattering or UV radiation) along with hyphenated detection and structural analysis methods (CD, NMR, melting temperature analysis and nanopore detection) were also applied for OG detection. Additionally, GQ-related computational simulations were also summarized. All these results emphasize that OG detection and the analysis of the effect of its presence in higher ordered structures like GQ is still a state-of-the-art research line with continuously increasing interest

Gliko és foszfopeptidek szintézisének lehetőségei = Synthesis of glyco and phosphopeptides

Módszereket dolgoztunk ki oligo-szachariddal glikozilált N-glikopeptidek szintéziséremind konvergens, mind építőkő módszerrel. Védőcsoportkombinációkat optimalizáltunk O-glikopeptidek szintézisére, valamint optimalizáltuk a kapcsolási reakciót a glikán és a védett aminosav között. Számos foszfopeptidet és sejtpenetráló peptidet szintetizáltunk, részben fluoreszcensen jelzett formában is. Új foldamer molekulát (N-amino prolin) állítottunk elő és építettünk be béta-aminosav oligomerekbe. Megvizsgáltuk a kapott oligomerek térszerkezeti és stabilitásviszonyait. | We improved the applicable methods for the synthesis of N-glycopeptides including convergent and building block approach. The protecting group combinations for the synthesis of O-glycopeptides was optimized and we improved the coupling conditions for the reaction of the glycosyl donor and acceptor. Numerous phospho and cell-penetrating peptide were synthesized and a part of them was fluorescently labelled. A new foldamer molecule (N-amino proline) was prepared and incorporated into beta-amino acid oligomers. The conformation and the stability of the new oligomers was investigated

Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates

Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5′ or 3′ end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation

A three-component reagent system for rapid and mild removal of O-, N- and S-trityl protecting groups

A new reagent system consisting of a Lewis acid such as BF3·Et2O or Cu(OTf)2, the mild protic acid hexafluoroisopropanol and the reducing quenching agent triethylsilane was elaborated for O-, N- and S-detritylation of nucleoside, carbohydrate and amino acid derivatives. The method is compatible with acetyl, silyl, acetal and Fmoc groups

Béta-amiloid peptidek aggregációja és kölcsönhatása fehérjékkel; új neuroprotektív vegyületek alkalmazása az Alzheimer-kór megelőzésére = Beta-amyloid aggregation and interaction with proteins; novel neuroprotective compounds for prevention of Alzheimer's disease

Új, standardizálható módszert dolgoztunk ki toxikus �béta-amiloid (Abéta) 1-42 peptid oligomerek előállítására, a preparált oligomereket fiziko-kémiai módszerekkel jellemeztük. Két új neuroprotektív peptidmimetikum vegyületcsaládot találtunk, ezek az anyagok megvédik a neuronokat az Alzheimer-kór (AK) állatmodelljében az Abéta neurotoxikus hatásától. Mindkét vegyületcsoportot szabadalmilag védjük, mint az AK potenciális gyógyszerjelölt vegyületeit. Új ex vivo módszert dolgoztunk ki az Abéta peptidek toxicitásának mérésére (patkány hippocampus szelet, MTT-teszt), a módszer alkalmas az új neuroprotektív vegyületeink aktivitásmérésére is. Az ex vivo hippocampus szeleteket sikerrel alkalmaztuk a neuronális plaszticitás (LTP) mérésére, az Abéta-toxicitás meghatározására, multielektród array (MEA) technikával. In vivo, egysejt-elvezetéses elektrofiziológiai mérésekkel bizonyítottuk az új peptidmimetikumaink neuroprotektív hatását. Proteomikai módszerekkel azonosítottuk az Abéta peptidekkel kölcsönhatásba lépő fehérjéket, ezek elsősorban plazmamembrán, ill. intraneuronális fehérjék (mitokondrium, endoplazmás reticulum, mikrotubuláris rendszer). Az intraneuronális fehérjék és az Abéta peptidek kölcsönhatásai kulcsszerepet játszhatnak az AK patogenezisében. Igazoltuk, hogy a Zn2+ ionok toxikus Abéta-aggregátumok képződését indukálják. Az AK transzgén állatmodelljén bizonyítottuk, hogy a Zn-kelátorok (pl. Perindopril) neuroprotektív hatásúak. Új AK-állatmodellt dolgoztunk ki az Abéta oligomerek icv bevitelével. | A new method was introduced for the preparation of toxic beta-amyloid (Abeta) 1-42 oligomers, these assemblies were characterized with physicochemical methods. Two families of novel neuroprotective peptidomimetics were found, these substances protect neurons against the toxic effect of Abeta in tg mouse models of Alzheimer’s disease (AD). Both groups of the novel substances will be patented as putative drug candidates for AD treatment. A new ex vivo method was introduced for toxicity measurement of Abeta peptides (rat hippocampal slices, MTT-assay); this method proved to be suitable for activity measurement of the novel neuroprotective substances. Hippocampal slices were successfully used for measurement of neuronal plasticity (LTP) for demonstrating neurotoxicity of Abeta aggregates, applying multielectrode array (MEA) technique. The neuroprotective effect of our novel peptidomimetics was demonstrated also in vivo, using one-cell electrophysiology. Proteomic methods were used for identification of proteins interacting with Abeta peptides; these are mainly plasma membrane and intraneuronal (mitochondrial, endoplasmatic reticular and microtubular) proteins. Interaction of intracellular proteins with Abeta may play key role in AD pathogenesis. The role of Zn2+ ions in formation of toxic Abeta-aggregates was demonstrated. Zn2+-chelators (e.g. Perindopril) were neuroprotective in a tg-mouse model of AD. A new AD rat model was introduced using icv administration of synthetic Abeta oligomers

Synthesis of Heterocycles and Nucleosides Forming Higher—Order Structures

Nucleic acid analogues play a multifaceted role in biology and materials science. Our efforts towards unveiling these roles led to xanthine derivatives that form higher–order structures with quadruplex-forming abilities. In this paper we present further modifications of the xanthine core resulting into 9-deaza and 8-aza-9-deaza heterocycles (pyrrolo[3,2-d]pyrimidines and pyrazolo[4,3-d]pyrimidines, respectively) that form tetrads and other higher–order structures. Additionally, the ring contraction of 5-fluoro-2′,3′-O-isopropylideneuridine gave rise to the formation of an imidazolidine-4-carboxylic acid nucleoside derivative. Our computational predictions forecasted that the latter derivative will form stable triads

The evaluation of 5-amino- and 5-hydroxyuracil derivatives as potential quadruplex-forming agents

© The Royal Society of Chemistry. 5-Substituted uracils (NH 2 or OH groups in position 5) have been examined theoretically and experimentally as potential building blocks in quadruplex structures. Our high level Density Functional Theory (DFT) calculations showed that the tetramer formation and stacking energies for 5-substituted uracils are similar to the energies of purine-based xanthine (X) or guanine (G) structures. As tetrads of 5-substituted uracils cover almost exactly the same area as purine tetrads, mixed tetrads or quadruplex structures based on X or G and 5-substituted uracil motifs are possible. According to the calculations, 5-hydroxyuracil-based structures are the best candidates for experimental implementation which was corroborated by the existence of higher complexes in the mass spectra of 1-benzyl-5-hydroxyuracil. These pyrimidine-based molecules can be used as efficient building blocks in different applications including aptamers, bio-sensors or-taking into account the larger cavity in the central region of 5-hydroxyuracil structures-as an artificial ion channel

Supramolecular ring structures of 7-methylguanine: a computational study of its self-assembly and anion binding

The density functional theory calculations of 7-methylguanine clusters revealed that stable ring assemblies can be formed with or without anions in the center position and hexameric clusters are the most stable and most planar ones. The coordination of anions (Cl−, Br−, NO3−) stabilizes and thus favors the formation of planar aggregates. We believe that the predicted planar structures stabilized by anions are good models for self-assembly structures formed at solid-liquid or solid-gas interfaces. Comparing the bonding and average H-bond energy to reference ribbon calculations we pointed out the presence of the previously introduced cooperativity effect in circular supramolecular structures of 7-methylguanine