Janez Plavec - Academia.edu (original) (raw)

Papers by Janez Plavec

Metabolites

Physical inactivity is a worldwide health problem, an important risk for global mortality and is ... more Physical inactivity is a worldwide health problem, an important risk for global mortality and is associated with chronic noncommunicable diseases. The aim of this study was to explore the differences in systemic urine 1H-NMR metabolomes between physically active and inactive healthy young males enrolled in the X-Adapt project in response to controlled exercise (before and after the 3-day exercise testing and 10-day training protocol) in normoxic (21% O2), normobaric (~1000 hPa) and normal-temperature (23 °C) conditions at 1 h of 50% maximal pedaling power output (Wpeak) per day. Interrogation of the exercise database established from past X-Adapt results showed that significant multivariate differences existed in physiological traits between trained and untrained groups before and after training sessions and were mirrored in significant differences in urine pH, salinity, total dissolved solids and conductivity. Cholate, tartrate, cadaverine, lysine and N6-acetyllisine were the most ...

Nucleic Acids Research

The AUTS2 gene has been shown to influence brain development by controlling the number of neurons... more The AUTS2 gene has been shown to influence brain development by controlling the number of neurons, promoting the growth of axons and dendrites and regulating neuronal migration. The expression of two isoforms of AUTS2 protein is precisely regulated and misregulation of their expression has been correlated with neurodevelopmental delay and autism spectrum disorder. A CGAG-rich region, which includes a putative protein binding site (PPBS), d(AGCGAAAGCACGAA), was found in the promoter region of AUTS2 gene. We show that oligonucleotides from this region adopt thermally stable non-canonical hairpin structures stabilized by G:C and sheared G:A base pairs arranged in a repeating structural motif we termed CGAG block. These motifs are formed consecutively, in a way that exploits a shift in register throughout the whole CGAG repeat to maximize the number of consecutive G:C and G:A base pairs. The differences in CGAG repeat shifting affect the structure of the loop region, where PPBS residues...

Handbook of Chemical Biology of Nucleic Acids

Molecules

The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, ... more The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-ROESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations, using Functional Density Theory (DFT). In addition, utilizing a combination of 2D-NOESY and 2D-ROESY spectra an exo structure was established for both of the analogs. This experimental results were confirmed by theoretical mechanistic studies, as the lowest minima conformations derived through DFT calculations were compatible with the spatial correlations observed in the 2D-NOESY and 2D-ROESY spectra. Finally, molecular binding experiments were performed to detect the potential targets for DKI21 and DKI24, derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for the most of the enzymes studied. The ADMET calculations, using the preADMET and pKCSm ...

Metabolites

Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one o... more Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants’ levels of urine and fecal proton nuclear magnetic resonance (1H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional gene...

Molecules

The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydr... more The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding ...

Abstract. It has previously been shown that r(GGA)4 folds into a G-quadruplex structure, which bi... more Abstract. It has previously been shown that r(GGA)4 folds into a G-quadruplex structure, which binds to the normal cellular form of the prion protein (PrPC) with high affinity. The current study utilizes CD and NMR spectroscopy to show that a dimeric parallel G-quadruplex structure is formed by r(GGA)2 in a KCl solution. Each r[(GGA)2]2 G-quadruplex unit exhibits two G-quartets, one of which is hydro-gen bonded to two additional adenines forming a hexade. Through stacking of hexade planes, two G-quadruplex units interact with each other and form a symmetric dimer, r[(GGA)2]4. The topology of r[(GGA)2]4 is in agreement with the fold of r[(GGA)4]2, however, subtle differences are found in the region responsible for PrPC binding.

Scientific Reports, 2017

Cyclic di-nucleotides (CDNs) are second messengers in bacteria and metazoan that are as such cont... more Cyclic di-nucleotides (CDNs) are second messengers in bacteria and metazoan that are as such controlling important biological processes. Here the conformational space of CDNs was explored systematically by a combination of extensive conformational search and DFT calculations as well as NMR methods. We found that CDNs adopt pre-organized conformations in solution in which the ribose conformations are North type and glycosidic bond conformations are anti type. The overall flexibility of CDNs as well as the backbone torsion angles depend on the cyclization of the phosphodiester bond. Compared to di-nucleotides, CDNs display high rigidity in the macrocyclic moieties. Structural comparison studies demonstrate that the pre-organized conformations of CDNs highly resemble the biologically active conformations. These findings provide information for the design of small molecules to modulate CDNs signalling pathways in bacteria or as vaccine adjuvants. The rigidity of the backbone of CDNs ena...

Journal of the American Chemical Society, Jan 2, 2018

Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases... more Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor ( VEGF) gene differed topologically from unoxidized G4. The oxidized VEGF G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guani...

Nature communications, Jan 17, 2017

Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical famili... more Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5'-AGCGA-3' tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5'-AGCGA-3' and 5'-GGG-3' repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular process...

Acta Chimica Slovenica, 2016

Nucleic Acids Research, 2015

Colloid and Polymer Science, 2015

Abstract1H NMR chemical shift, line width, indirect nuclear splitting value, peak area integratio... more Abstract1H NMR chemical shift, line width, indirect nuclear splitting value, peak area integration value, and spin–lattice and spin–spin relaxation times at 298 K are compared for low-concentration isotropic solutions of n-octylammonium n-octadecanoate prepared via different techniques and conditions using dried, distilled, and degassed deuterochloroform and the nontreated solvent containing tetramethylsilane. The nature of the variation of observed spectral parameters and relaxation/rotational behavior with chemical composition (presence of oxygen and other paramagnetic species, stabilizer, impurities, and degradation products) of the solvent, history of the solution, and sample containment are analyzed. Relaxation times are interpreted in terms of monomer structure and reorientation and internal rotation modes as a function of atomic position along the n-alkyl chains. Collectively, the relaxation behavior of the surfactant complies with the two-step model of fast picosecond internal rotations of different size segments containing methylene groups separated in timescale from slower large segment and overall molecular tumbling modes of the monomer. Fast motional phenomena do not appear to be appreciably influenced by the chemistry of the solvent in contrast to spectral parameters such as chemical shift and line width of the labile ammonium protons. A model is also presented to explain anomalous variation of the peak area integration value with chemical shift of the ammonium resonance peak.

Croatica Chemica Acta, 2014

Tetrahedron Letters, 1993

Tetrahedron, 2004

Recently, we have prepared a novel class of DNA analogues containing the [3′-NH–P(CH3)(O)–O-5′] m... more Recently, we have prepared a novel class of DNA analogues containing the [3′-NH–P(CH3)(O)–O-5′] methanephosphonamidate linkage. Synthesis of such analogues requires preparation of the dinucleoside methanephosphonamidates N×N, where N is a 2′-deoxyribonucleoside moiety and × is the methanephosphonamidate linkage. Dimers T×T and C×T were obtained in a non-stereospecific manner giving rise to a pair of P-chiral diastereomers. Such diastereomers were effectively

Rapid Communications in Mass Spectrometry, 1992

Metabolites

Physical inactivity is a worldwide health problem, an important risk for global mortality and is ... more Physical inactivity is a worldwide health problem, an important risk for global mortality and is associated with chronic noncommunicable diseases. The aim of this study was to explore the differences in systemic urine 1H-NMR metabolomes between physically active and inactive healthy young males enrolled in the X-Adapt project in response to controlled exercise (before and after the 3-day exercise testing and 10-day training protocol) in normoxic (21% O2), normobaric (~1000 hPa) and normal-temperature (23 °C) conditions at 1 h of 50% maximal pedaling power output (Wpeak) per day. Interrogation of the exercise database established from past X-Adapt results showed that significant multivariate differences existed in physiological traits between trained and untrained groups before and after training sessions and were mirrored in significant differences in urine pH, salinity, total dissolved solids and conductivity. Cholate, tartrate, cadaverine, lysine and N6-acetyllisine were the most ...

Nucleic Acids Research

The AUTS2 gene has been shown to influence brain development by controlling the number of neurons... more The AUTS2 gene has been shown to influence brain development by controlling the number of neurons, promoting the growth of axons and dendrites and regulating neuronal migration. The expression of two isoforms of AUTS2 protein is precisely regulated and misregulation of their expression has been correlated with neurodevelopmental delay and autism spectrum disorder. A CGAG-rich region, which includes a putative protein binding site (PPBS), d(AGCGAAAGCACGAA), was found in the promoter region of AUTS2 gene. We show that oligonucleotides from this region adopt thermally stable non-canonical hairpin structures stabilized by G:C and sheared G:A base pairs arranged in a repeating structural motif we termed CGAG block. These motifs are formed consecutively, in a way that exploits a shift in register throughout the whole CGAG repeat to maximize the number of consecutive G:C and G:A base pairs. The differences in CGAG repeat shifting affect the structure of the loop region, where PPBS residues...

Handbook of Chemical Biology of Nucleic Acids

Molecules

The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, ... more The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-ROESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations, using Functional Density Theory (DFT). In addition, utilizing a combination of 2D-NOESY and 2D-ROESY spectra an exo structure was established for both of the analogs. This experimental results were confirmed by theoretical mechanistic studies, as the lowest minima conformations derived through DFT calculations were compatible with the spatial correlations observed in the 2D-NOESY and 2D-ROESY spectra. Finally, molecular binding experiments were performed to detect the potential targets for DKI21 and DKI24, derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for the most of the enzymes studied. The ADMET calculations, using the preADMET and pKCSm ...

Metabolites

Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one o... more Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants’ levels of urine and fecal proton nuclear magnetic resonance (1H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional gene...

Molecules

The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydr... more The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding ...

Abstract. It has previously been shown that r(GGA)4 folds into a G-quadruplex structure, which bi... more Abstract. It has previously been shown that r(GGA)4 folds into a G-quadruplex structure, which binds to the normal cellular form of the prion protein (PrPC) with high affinity. The current study utilizes CD and NMR spectroscopy to show that a dimeric parallel G-quadruplex structure is formed by r(GGA)2 in a KCl solution. Each r[(GGA)2]2 G-quadruplex unit exhibits two G-quartets, one of which is hydro-gen bonded to two additional adenines forming a hexade. Through stacking of hexade planes, two G-quadruplex units interact with each other and form a symmetric dimer, r[(GGA)2]4. The topology of r[(GGA)2]4 is in agreement with the fold of r[(GGA)4]2, however, subtle differences are found in the region responsible for PrPC binding.

Scientific Reports, 2017

Cyclic di-nucleotides (CDNs) are second messengers in bacteria and metazoan that are as such cont... more Cyclic di-nucleotides (CDNs) are second messengers in bacteria and metazoan that are as such controlling important biological processes. Here the conformational space of CDNs was explored systematically by a combination of extensive conformational search and DFT calculations as well as NMR methods. We found that CDNs adopt pre-organized conformations in solution in which the ribose conformations are North type and glycosidic bond conformations are anti type. The overall flexibility of CDNs as well as the backbone torsion angles depend on the cyclization of the phosphodiester bond. Compared to di-nucleotides, CDNs display high rigidity in the macrocyclic moieties. Structural comparison studies demonstrate that the pre-organized conformations of CDNs highly resemble the biologically active conformations. These findings provide information for the design of small molecules to modulate CDNs signalling pathways in bacteria or as vaccine adjuvants. The rigidity of the backbone of CDNs ena...

Journal of the American Chemical Society, Jan 2, 2018

Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases... more Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor ( VEGF) gene differed topologically from unoxidized G4. The oxidized VEGF G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guani...

Nature communications, Jan 17, 2017

Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical famili... more Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5'-AGCGA-3' tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5'-AGCGA-3' and 5'-GGG-3' repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular process...

Acta Chimica Slovenica, 2016

Nucleic Acids Research, 2015

Colloid and Polymer Science, 2015

Abstract1H NMR chemical shift, line width, indirect nuclear splitting value, peak area integratio... more Abstract1H NMR chemical shift, line width, indirect nuclear splitting value, peak area integration value, and spin–lattice and spin–spin relaxation times at 298 K are compared for low-concentration isotropic solutions of n-octylammonium n-octadecanoate prepared via different techniques and conditions using dried, distilled, and degassed deuterochloroform and the nontreated solvent containing tetramethylsilane. The nature of the variation of observed spectral parameters and relaxation/rotational behavior with chemical composition (presence of oxygen and other paramagnetic species, stabilizer, impurities, and degradation products) of the solvent, history of the solution, and sample containment are analyzed. Relaxation times are interpreted in terms of monomer structure and reorientation and internal rotation modes as a function of atomic position along the n-alkyl chains. Collectively, the relaxation behavior of the surfactant complies with the two-step model of fast picosecond internal rotations of different size segments containing methylene groups separated in timescale from slower large segment and overall molecular tumbling modes of the monomer. Fast motional phenomena do not appear to be appreciably influenced by the chemistry of the solvent in contrast to spectral parameters such as chemical shift and line width of the labile ammonium protons. A model is also presented to explain anomalous variation of the peak area integration value with chemical shift of the ammonium resonance peak.

Croatica Chemica Acta, 2014

Tetrahedron Letters, 1993

Tetrahedron, 2004

Recently, we have prepared a novel class of DNA analogues containing the [3′-NH–P(CH3)(O)–O-5′] m... more Recently, we have prepared a novel class of DNA analogues containing the [3′-NH–P(CH3)(O)–O-5′] methanephosphonamidate linkage. Synthesis of such analogues requires preparation of the dinucleoside methanephosphonamidates N×N, where N is a 2′-deoxyribonucleoside moiety and × is the methanephosphonamidate linkage. Dimers T×T and C×T were obtained in a non-stereospecific manner giving rise to a pair of P-chiral diastereomers. Such diastereomers were effectively

Rapid Communications in Mass Spectrometry, 1992