SgrAI is a restriction endonuclease (ENase) that cuts a long recognition sequence and exhibits self-modulation of cleavage activity and sequence specificity. Previous research has shown that SgrAI forms large oligomers when bound to particular DNA sequences and under the same conditions where SgrAI exhibits accelerated DNA cleavage kinetics. However, the detailed structure and stoichiometry of SgrAI:DNA as well as the basic building block of the oligomers, has not been fully characterized. Ion mobility mass spectrometry (IM-MS) was employed to analyze SgrAI/DNA complexes and show that the basic building block of the oligomers is the DNA-bound SgrAI dimer (DBD). The oligomers are heterogeneous containing a mixture of species with variable numbers of DBD. The collision cross sections (CCS) of the oligomers were found to have a linear relationship with the number of DBD. Models of the SgrAI/DNA oligomers were constructed and a head-to-tail arrangement was most consistent with the experimental CCS.

Cationic lipids are efficient tools to introduce nucleic acids and proteins into cells. Elucidation of the mechanism and cellular pathways associated to such a transport has been relatively slow, even though significant progress has been made in the characterization of the intracellular trafficking of cationic lipid/DNA complexes. Surprisingly, little is known about the effects of these delivery vectors on cell functioning. In the present thesis, we show that cationic lipids and cationic lipid/DNA complexes strongly increase the intracellular Ca2+ concentration. The end point of the Ca2+ increase was ~400 nM from a basal level of ~100 nM. The [Ca2+]i increase was studied using K562 and Jurkat cells cultured in vitro. This effect is weakened following addition of DNA to cationic liposomes, although remaining very large at cationic lipid/DNA ratios commonly used for cell transfection experiments. Removal of extracellular Ca2+ did not abolish this effect significantly and preincubating K562 cells with the Ca2+-ATPase inhibitor thapsigargin strongly abolished intracellular Ca2+ concentration increase, indicating that Ca2+ was released mainly from internal Ca2+ stores sensitive to thapsigargin. Pretreatment of the cells with the phospholipase C inhibitor U73122 blocked the intracellular Ca2+ concentration rise, suggesting an inositol pathway-dependent mechanism. LDH release assay indicates that in the conditions used for fluorescence measurement and in those used to transfer DNA into cells, cationic liposomes diC14-amidine and DOTAP had no massive cytotoxic effects. Cationic liposomes showed more toxicity than their corresponding complexes; this toxicity decreases in the presence of serum. The effect of cationic lipids on phosphatidylinositol-specific phospholipase C (PI-PLC) was quantitatively assessed using phosphatidylinositol (PI) and radiolabeled phosphatidylinositol ([3H]-PI). Incorporation of diC14-amidine into PC/PI vesicle activated PI-PLC and was shown to activate the hydrolysis of PI and [3H]-PI. Our data may suggest that mobilization of intracellular Ca2+ by complex could have an effect on the transfection process itself. These results indicate for the first time that cationic lipids and cationic lipid/DNA complexes are not inert and can affect the functioning of the cells by increasing their intracellular Ca2+.

The main goals of the thesis are advanced characterization by complementary optical and electrical methods of organic semiconductors and the complexes of DNA (deoxyribonucleic acid) designed with purposefully controllable properties for opto-, photo- and electrical applications in modern device engineering. It was demonstrated that the polymer photovoltaic device having an active layer with donor/transmitter/acceptor structure bearing polar molecules exhibits the improvement of the external quantum efficiency associated with the growth of the mobility and reduced potential barrier for charge injection or extraction from the electrodes. The impact of the trapping states and their energetical and spatial distribution on the charge transport properties of organic semiconductors was revealed by several different complementary methods. It was demonstrated that carrier trapping is effectively involved in the charge transport phenomena, depending on the exciting light spectral range and applied electrical field. The influence of the hybrid DNA, dyes and silica material complexes on the optical properties of bio-organic materials was proven. Later the new cationic surfactant with a high efficiency third order nonlinear optical properties was demonstrated, which extended the range of available solvents for DNA complex. / Disertacija skirta išanalizuoti veiksnius, įtakojančius krūvio pernašą ir pagavimą šiuolaikinėse organinėse medžiagose skirtose optoelektronikai, bei ištirti DNR bio-molekulių įtaką elektrinėms bei optinėms medžiagų savybėms. Eksperimentiškai nustatyta, kad polimerinės medžiagos turinčios aktyviojo sluoksnio struktūrą: donoras/pernašos grandis/akceptorius ir chemiškai sujungtos su polinėmis molekulėmis, pasižymi išorinio kvantinio našumo padidėjimu, susijusiu su judrio išaugimu ir sumažėjusiu potencialo barjeru krūvininkų injekcijai ar ekstrakcijai iš elektrodų. Panaudojant keletą skirtingų, bet papildančių eksperimentinių metodų, parodyta pagavimo būsenų ir jų energetinio bei erdvinio pasiskirstymo įtaka krūvininkų pernašos savybėms organiniuose puslaidininkiuose. Pademonstruota, kad krūvininkų pagavimas efektyviai lemia krūvio pernašos reiškinius ir priklauso nuo žadinančios šviesos spektro pločio bei pridėto elektrinio lauko. Nustatyta DNR komplekso, sudaryto iš dažo ir silikagelio matricos, įtaka optinėms medžiagos savybėms. Taip pat pademonstruoti nauji katijoniniai surfaktantai su efektyviomis trečios eilės netiesinės optikos savybėmis, kurie išplečia tirpiklių pasirinkimą gaminant DNR kompleksus.

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Komplexe aus entgegengesetzt geladenen Polyelektrolyten haben sowohl in der Biologie als auch in den Materialwissenschaften eine große Bedeutung. Im Mittelpunkt des Interesses stehen besonders die Kondensation der DNA in vitro, die Struktur des Nukleosoms im Zellkern, nicht-virale Systeme zur Transfektion von DNA in Zellen oder der Vorgang der layer-by-layer Adsorption. Verschiedene Theorien befassen sich mit den treibenden Kräften solcher Komplexbildungen. Allerdings standen experimentelle Untersuchungen auf diesem Gebiet bisher noch aus. Dieser Arbeit liegt die Fragestellung zu Grunde, ob es mit Hilfe der Rasterkraftmikroskopie möglich ist, die Struktur einzelner Polyelektrolytkomplexe, bestehend aus den beiden Polyelektrolyten DNA und dendronisierten Polymer, aufzuklären und ihre Komplexbildung zu untersuchen. Die Komplexe bildeten sich in Lösung und wurden anschließend auf einer unbeschichteten oder mit positiven Polymeren beschichteten Glimmeroberfläche adsorbiert. Auf der positiv beschichteten Glimmeroberfläche hafteten DNA-dendronisierte Polymer Komplexe mit einem Ladungsverhältnis von 1:1 bis 1:0.7 (DNA:dendronisiertes Polymer). Anhand der hochaufgelösten rasterkraftmikroskopischen Aufnahmen wurde ein Modell entwickelt, das die Umwicklung der DNA um das dendronisierte Polymer beschreibt. Der DNA-DNA Abstand ergab sich zu (2.30 ± 0.27) nm für den Komplex mit DNA und zweiter Generation dendronisierter Polymere und zu (2.16 ± 0.27) nm mit vierter Generation. Die theoretische Vorhersage der Überladung der Komplexe konnte experimentell bestätigt werden. Mit Hilfe der Rasterkraftmikroskopie konnte überdies der Einfluss des Salzgehaltes der Lösung auf die Bildung der Komplexe mit DNA und zweiter Generation dendronisierter Polymere untersucht werden. Wie man anhand des Zusammenwirkens von elektrostatischen Kräften und entropischen Wechselwirkungen bei der Adsorption von Polyelektrolyten vorhersagen kann, durchlief der DNA-DNA Abstand ein Minimum bei ansteigendem Salzgehalt. Bei sehr hohem Salzgehalt (2.4 M NaCl) konnte das Ablösen der DNA von dem Komplex beobachtet werden. Die untersuchten DNA/dendroniserten Polymer Komplexe bilden ein neues Modellsystem, mit dem einzelne Polyelektrolyt-Wechselwirkungen direkt untersucht werden können. Ein Vergleich der experimentellen Daten mit den vorhandenen Theorien zeigte, dass der Prozess des Überladens weitgehend durch elektrostatische Wechselwirkung zwischen den beiden Polyelektrolyten beschrieben werden kann. Sowohl entropische Beiträge als auch die Biegeenergie der umwickelnden DNA sind vernachlässigbar. Basierend auf diesen Ergebnissen können neue Trägerstrukturen für effizientere nicht-virale DNA-Transfektionssysteme entwickelt werden. / Complexes of oppositely charged polyelectrolytes play an important role in both biology and material science, for instance DNA condensation in vitro, nucleosomal structure, non-viral gene transfection systems as well as layer-by-layer adsorption. Although there are theories predicting overcharging of polyelectrolyte complexes, the driving forces are still under debate and systematic experimental studies on single polyelectrolytes remain challenging. Therefore the question arose if it is possible to analyze single polyelectrolyte complexes, using DNA and dendronized polymers, with the scanning force microscope in order to investigate the complexation in detail. For the complex analysis, the polyelectrolytes were allowed to interact in solution and then to adsorb on negatively charged mica or on mica coated with a positively charged polymer. Scanning force microscopy was used to investigate the adsorbed species. DNA/dendronized polymer complexes of charge ratio of 1/1 through 1/0.7 adsorbed on mica coated with a positively charged polymer. The analysis of high resolution molecular images indicated that DNA wraps around the dendronized polymer with an estimated pitch of (2.30 ± 0.27) nm and (2.16 ± 0.27) nm for dendronized polymers of generation two and four, respectively. In the proposed model the polyelectrolyte with the smaller linear charge density is wrapped around the more highly charged dendronized polymer, resulting in a negatively overcharged complex. This overcharging is consistent within recent theories of spontaneous overcharging of complexes of one polyelectrolyte wrapping around the other. Using the complex of DNA and dendronized polymers of second generation, the influence of monovalent salt concentration on the molecular structure was studied. By increasing the salt concentration the pitch showed a minimum as predicted by the interplay of electrostatic forces and entropic interactions of polyelectrolyte adsorption. At high salt concentration (2.4 M NaCl) the release of DNA from the complex can be observed. The results showed that the DNA/dendronized polymer system can be used as a new, high potential model system to investigate single polyelectrolyte interactions. With regard to recent theories, the experimental results indicate that the overcharging of the complex is mainly driven by electrostatic forces whereas contributions of counterion entropy and bending energy seem to be negligible. This understanding may be useful for the design of single polyelectrolyte complexes for non-viral gene delivery systems and might help to optimize the transfection efficiency based on the structure of the vector system.

Cationic lipids are efficient tools to introduce nucleic acids and proteins into cells. Elucidation of the mechanism and cellular pathways associated to such a transport has been relatively slow, even though significant progress has been made in the characterization of the intracellular trafficking of cationic lipid/DNA complexes. Surprisingly, little is known about the effects of these delivery vectors on cell functioning. In the present thesis, we show that cationic lipids and cationic lipid/DNA complexes strongly increase the intracellular Ca2+ concentration. The end point of the Ca2+ increase was ~400 nM from a basal level of ~100 nM. The [Ca2+]i increase was studied using K562 and Jurkat cells cultured in vitro. This effect is weakened following addition of DNA to cationic liposomes, although remaining very large at cationic lipid/DNA ratios commonly used for cell transfection experiments. Removal of extracellular Ca2+ did not abolish this effect significantly and preincubating K562 cells with the Ca2+-ATPase inhibitor thapsigargin strongly abolished intracellular Ca2+ concentration increase, indicating that Ca2+ was released mainly from internal Ca2+ stores sensitive to thapsigargin. Pretreatment of the cells with the phospholipase C inhibitor U73122 blocked the intracellular Ca2+ concentration rise, suggesting an inositol pathway-dependent mechanism. LDH release assay indicates that in the conditions used for fluorescence measurement and in those used to transfer DNA into cells, cationic liposomes diC14-amidine and DOTAP had no massive cytotoxic effects. Cationic liposomes showed more toxicity than their corresponding complexes; this toxicity decreases in the presence of serum. The effect of cationic lipids on phosphatidylinositol-specific phospholipase C (PI-PLC) was quantitatively assessed using phosphatidylinositol (PI) and radiolabeled phosphatidylinositol ([3H]-PI). Incorporation of diC14-amidine into PC/PI vesicle activated PI-PLC and was shown to activate the hydrolysis of PI and [3H]-PI. Our data may suggest that mobilization of intracellular Ca2+ by complex could have an effect on the transfection process itself. These results indicate for the first time that cationic lipids and cationic lipid/DNA complexes are not inert and can affect the functioning of the cells by increasing their intracellular Ca2+. <p><p> / Doctorat en sciences, Spécialisation chimie / info:eu-repo/semantics/nonPublished

The binding of different proteins involved in processes such as transcription, replication and chromatin compaction to regions of the genome is regulated by the structure of DNA. Thus, DNA structure acts as the crucial link modulating evolutionary selection of the DNA sequence based on its own function, and the function of the proteins it encodes. The aim of this work is to examine the role of intrinsic, sequence-dependent structural variations vis-a -vis the protein-induced variations, in allowing DNA to assume geometries necessary for binding by proteins. For this purpose, we carried out analyses of datasets of X-ray crystal structures of free and protein-bound DNA, and molecular dynamics simulation studies of few free DNA structures and a protein-DNA complex. Each of the projects described below will appear as a separate chapter in the thesis. Analysis of X-ray crystal structure datasets Dataset of high-resolution X-ray crystal structures of free and protein-bound DNA This project was initiated with the aim of investigating the variation in A-and B-forms of DNA and the role they play in the binding of proteins. However, a survey of the existing literature indicated that the terms ‘A-DNA’ and ‘B-DNA’ were being used rather loosely and several different parameters at the local structural level were being used by various investigators to characterise these structures. Hence a systematic study was taken up to analyse all high-resolution free DNA structures comprising of sufficient number of contiguous Watson-Crick basepairs, irrespective of how they were classified by the existing databases. We also carried out a study of double-helical, Watson-Crick basepaired, free RNA structures for comparison. The structures in the RNA dataset were observed to rigidly assume the A-form and hence the average values of different parameters for that dataset were used to characterise the A-form. The analysis of free DNA and RNA structures was accompanied by an analysis of protein-bound DNA crystal structures. DNA structures bound to the helix-turn-helix motif in proteins were also analysed separately. The analysis of free DNA and RNA structures allowed us to pinpoint the parameters suitable for discriminating A-and B-forms of DNA at the local structural level. The results illustrated that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A-and the B-forms. Most protein-bound DNA structures, including those with large, smooth curvature, were observed to assume the B-form. The A-form was observed to be limited to a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. Thus our study highlighted the structural versatility of B-form DNA, which allowed it to take up a range of global geometries to accommodate most DNA-binding protein motifs. Dataset of X-ray crystal structures of the nucleosome The study of high-resolution structures of free and protein-bound DNA was followed by an analysis of a dataset of X-ray crystal structures of the nucleosome, which is the fundamental repeating unit of the eukaryotic chromosome, and has been shown to play an important role in transcription regulation. Our results indicated that there is an ensemble of dinucleotide and trinucleotide level parameters that can give rise to similar global nucleosome structures. We therefore raise doubts about the use of the best resolved nucleosome structure as the template to calculate the energy required by putative nucleosome-forming sequences for adopting the nucleosome structure. Based on our results, we have proposed that the local and global level structural variability of DNA may act as a significant factor influencing the formation of nucleosomes in the vicinity of high-plasticity genes, and in determining the probability of binding by regulatory proteins. Molecular dynamics simulation studies of free and protein-bound DNA structures The analysis of crystal structure databases was complemented by molecular dynamics (MD) studies to investigate the dynamic evolution of the DNA structure in its free and protein-bound states. The following three simulation studies were carried out: Study to examine the biological relevance of the presence of 5-methyl group in thymine nucleotides An investigation of the biological relevance of the 5-methyl group in thymine nucleotides was carried out. For this purpose, comparison of molecular dynamics studies on structures with sequences d(CGCAAAUUUGCG)2and d(CGCAAATTTGCG)2was carried out. Our results showed that the presence of the thymine 5-methyl group was necessary for the A-tract to assume characteristic properties such as a narrow minor groove. It was also shown to modulate local level structural parameters and consequently, the curvature of the longer DNA fragment in which the A-tract was embedded. The analysis also provided possible explanation for the experimentally observed interaction of A-tracts with drugs and DNase-I in the presence and the absence of the thymine 5-methyl group. This project was the first of a series of MD studies, and hence several protocols were tested before finalising the correct protocol. Simulations were carried out using the Berendsen temperature equilibration scheme as well as the Langevin temperature equilibration scheme on both the structures. The Langevin temperature equilibration scheme was found to be unsuitable for nucleic acid simulations, as it caused long-term and possibly permanent disruption of the double-helical structure at the terminal and the neighbouring two positions in the sequence. The Berendsen temperature equilibration scheme was not observed to cause such disruptions. Simulations were also carried out on both structures, with or without initialising the initial ion positions. The position of minimum electrostatic potential, where AMBER8 placed the first counterion, was observed to act as a minimum energy trap from which the counterion could not escape even during the course of several nanoseconds of simulation. Hence, the actual simulations were carried out using the Berendsen temperature equilibration scheme, and after randomisation of initial ion positions. The results of protocol testing have been reported in an appendix. Study of DNA bending and curvature An analysis of DNA bending and curvature was carried out, by MD simulation on structures of three, ∼thirty basepair long sequences, namely, d(G-3(CA4T4G)-C)2, d(G-3(CT4A4G)-C)2and d(T-GACTA5T-GACTA6T-GACTA5T-G). For each molecule, snapshots belonging to a particular global geometry (linear, curved, bent in a particular direction etc.) were grouped together, and the average values of the dinucleotide step parameters for different groups were compared. It was observed that for all the three molecules, the average values for groups corresponding to different global geometries were within 1of each other, indicating that ensemble average values of dinucleotide level parameters are incapable of predicting the global geometry of a DNA molecule. Study of the TraR-Trabox complex The study on DNA bending and curvature was followed by simulations of a protein-DNA complex comprising of the bacterial quorum sensing transcription factor TraR with its promoter region known as Trabox. Simulations of a protein-free wild-type Trabox and a Trabox with two mutations in the spacer region were also carried out. Grouping of DNA snapshots in all the three simulations based on average values of dinucleotide parameters in the spacer region shows how selection of the ‘right’ DNA geometry by proteins works at several levels. The number of snapshots of free mutated Trabox assuming a geometry favourable for protein-binding in terms of average twist alone are less than one-fourth of the corresponding number for free wild-type Trabox. When one applies further selection criteria in terms of other parameters such as roll and slide, the number of mutated Trabox snapshots with a geometry favourable for protein-binding drops to less than 0.5%ofthe total number of MD snapshots. Thus our results highlight how sequence-dependent changes in the structrure of DNA regions, adjacent to those that directly hydrogen-bond to proteins, can also critically influence processes such as transcription. General Conclusion Overall, our results indicate that intrinsic, sequence-dependent structural variations in free B-DNA allow it to sample a large volume of the double-helical conformational space, and assume global geometries that can accomodate most DNA-binding proteins.

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

The main aim of this work was to compare the genotoxicity of organic extracts from different size fractions of aerosol particles (1-10 µm, 0,5-1 µm, 0,17-0,5 µm) collected by high volume cascade impactors in various localities of the Czech Republic differing in the extent of the environmental pollution (Březno - strip mine, Dobré Štěstí - highway, Praha - city center, Láz - background station). Genotoxicity was determined in acellular assay of calf thymus DNA (CT-DNA) with and without S9 metabolic activation by analysis of DNA adducts induced by extractable organic matter (EOM) from the particulate matter (PM) by 32 P-postlabeling and the ability of extracts to induce oxidative DNA damage was evaluated using the competitive ELISA test. The main finding of this work is that most of the observed genotoxicity is connected with fine particles (<1 µm). The concentration of carcinogenic polycyclic aromatic hydrocarbons (c-PAHs) in EOMs indicate that fine fractions bound the highest amount of c-PAHs in all sampling sites. This fact might be related to a higher specific surface of this fraction as compared with a course fraction and a higher mass as compared with a condensational fraction. As for aerosol mass, both fine and condensational fractions are effective carriers of c-PAHs. Similarly, the DNA...