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Electrodeposited Coatings at ITO/FTO Enhancing their Applicability in Electroanalysis
Daňhel, Aleš ; Fojta, Miroslav
Recent possibilities of modification of transparent electrodes based on indium-tin oxide and/or fluorine doped tin oxide by electrodeposited coatings enhancing their electrochemical applicability in electroanalysis are discussed in this work. Ordered mesoporous silica and/or chemically functionalized mesoporous silica thin films may serve, among the common utilization in solid phase extraction, as protective layer of the electrode surface against its fouling and/or as molecular sieve permeable for small molecules and blocking large ones (DNA, proteins, etc.). Furthermore an electrodeposition of organic modifiers and/or metal (nano) particles inside of the ordered silica nanochanels together with direct electrodeposition of selected metal (nano) particles onto selected conductive transparent supports are presented here as well.
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Raman microspectroscopy of living cells and biological tissues
Moudříková, Šárka ; Mojzeš, Peter (advisor) ; Matthäus, Christian (referee) ; Samek, Ota (referee)
Title: Raman microspectroscopy of living cells and biological tissues Author: Šárka Moudříková Department / Institute: Institute of Physics of Charles University Supervisor of the doctoral thesis: doc. RNDr. Peter Mojzeš, CSc., Institute of Physics of Charles University Abstract: Raman microscopy combines Raman spectroscopy with optical confocal microscopy and thus provides information on chemical composition of a sample with a µm3 resolution. In this thesis, Raman microscopy has been used to study microalgae-unicellular photosynthetic organisms that are greatly relevant for the Earth's environment as well as for biotechnological applications. Raman microscopy of photosynthetic organisms struggles with a highly intensive background of the spectra, which is formed by fluorescence of cellular photosynthetic apparatus. In this thesis, we have developed a fast and reliable photobleaching method that suppresses the unwanted background; this method has enabled us to study intracellular distribution of algal biomolecules such as proteins, starch, lipids and polyphosphate. We have investigated an evolution of these structures during a cell cycle of a model microalga Desmodesmus quadricauda. Next, we have developed a method for quantitative analysis of polyphosphate in a cellular culture of a microalga Chlorella...
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Computational Study of the Properties and Reactivity of Bioinroganic Transition Metal Complexes
Baxová, Katarína ; Burda, Jaroslav (advisor) ; Sochorová Vokáčová, Zuzana (referee)
This work is focused on the reactions of diaqua-tetrakis(μ-acetylato)dirhodium(II,II) with guanine, that shows anti-cancer activities. Guanine can bond to the complex either by oxygen O6 or by nitrogen N7. We studied three possible versions of the system - one that is protonated on guanine, one protonated on the paddle-wheel and a neutral one. For all 6 reactions transition structures were found. For reactants, tranzition states and products we computed the values of electron density in the critical points of bonds, partial atom charges and the interaction energies of the system, guanine and water on the b3lyp/aug-cc- pvdz level. Pseudobasis and pseudopotentials were employed in the case of rhodium atom. For all the reactions thermodynamical properties were computed. Powered by TCPDF (www.tcpdf.org)
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Non-resonant Raman Spectroscopic Study of Guanine Quadruplex Structures
Golan, Martin ; Mojzeš, Peter (advisor) ; Mašek, Vlastimil (referee)
Parts of human telomere sequences containing at least 4 guanine subsequences show the ability to form intrastrand quadruplexes of remarkable conformational diversity. Former studies using conventional Raman spectroscopy have revealed that the sequence G3(TTAG3)3 at milimolar concentrations in phosphate buffer solution doped with Na+ ions (ionic strength 150 mM) adopts antiparallel conformation regardless of the length of standing at room temperature or annealing, whereas K+ ions cause gradual transition to "3+1" or even parallel conformation. On the other hand, measurements carried out upon sequence AG3(TTAG3)3 at similar concentrations using Photonic Crystal Fibre-enhanced Raman Spectroscopy (PCFRS) suggest that in the respective presence of both Na+ and K+ (ionic strength 100 mM), a parallel structure is adopted. The hereby presented work employs conventional Raman spectroscopy and Drop Coating Deposition Raman spectroscopy to examine the sequence AG3(TTAG3)3 at concentrations ranging from units to hundreds of milimoles in strands. It concludes that the structure adopted in the presence of Na+, resp. K+ ions is antiparallel, resp. "3+1", and doesn't change over time despite both long standing and annealing. Two hypotheses about the cause of the differences between the results obtained by PCFRS and...
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Quantum chemical study of the electron properties of various platinum(IV) complexes and their reaction mechanisms
Šebesta, Filip ; Burda, Jaroslav (advisor) ; Straka, Michal (referee)
It has been proven that platinum complexes are active in anticancer treatment as well as several other transition metals complexes. There is an effort in recent medicine to replace cisplatin complexes by drugs with smaller side effects. This work focuses on the reaction of 5'-dGMP (2'-deoxyguanosine-5'˗monophosphate) and cGMP (cyclic 2'-deoxyguanosine- monophosphate) with a platinum complex PtIV (dach)Cl4 (dach=diaminocyclohexane). In these two cases the Pt(IV) complex is only reduced in the presence of 5'-dGMP. The first part of the explored mechanism is the substitution reaction where a coordinate-covalent bond between platinum and nitrogen N7 of guanine is formed. In the next step oxygen of phosphate group is transferred to the C8 site. Subsequently the Pt(IV) complex is reduced. The final products represent 8˗oxo˗GMP and PtII (dach)Cl2, which are active in anticancer treatment in comparison with the kineticly inert reactant. The substitution of a chloride anion ends the reaction path for cGMP forming PtIV (dach)Cl3(N7-cGMP) complex. The structures were optimized at the DFT level with B3LYP functional in the basis set 6-31G(d) and PCM/UA0 solvation model. The energy parameters were computed at the B3LYP/6˗311++G(2df,2pd) level in the IEFPCM/sUAKS solvation model. Finally, the rate constants were...
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Biologically important non-canonical structures of nucleic acids in complexes with cationic porphyrins
Palacký, Jan ; Mojzeš, Peter (advisor) ; Setnička, Vladimír (referee) ; Víglaský, Viktor (referee)
Guanine quadruplexes are a class of unusual nucleic acids conformations based on stacked planar guanine tetrads stabilized via Hoogsteen pairing and cation coordination. They are implicated in numerous cellular processes including replication, recombination or transcription. Guanine quadruplexes are widespread within the human genome but their occurrence is highest in the single stranded guanine-rich regions at telomeres. Telomeric guanine quadruplexes are gaining growing interest due to their ability to inhibit the activity of the telomerase enzyme, which is responsible for the proliferation of tumor cells. Specifically, we investigated the conformational polymorphism of the human core telomeric sequence G3(TTAG3)3 conditioned by the concentration of DNA, metal cations (K+ , Na+ ) and/or annealing. Raman spectroscopy was employed as the primary method for this study because, unlike common spectroscopic methods, it allowed us to monitor the quadruplex structure at very high DNA concentrations mimicking molecular crowding conditions in the cell. We demonstrate that the G3(TTAG3)3 quadruplex switch between the antiparallel and parallel strand alignment as a function of nucleoside and potassium concentration. In addition, we demonstrate that cationic porphyrins can be used as sensitive probes of the quadruplex...
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Searching adenine and guanine rich regions
Vlachynská, Alžběta ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This work deals with searching adenine and guanine rich regions. Their finding which determines the randomness and functionality may lead to better understanding genetic data storage in DNA sequences. The first part of the work describes the chemical composition and structure of DNA, its replication, transcription and translation. It contains the basic information about the genome. The next chapter deals with numerical representation of DNA sequences, necessary for a computer processing. Nucleotide density is a method suitable for searching adenine and guanine rich regions. The practical part of the work is an application designed and implmented in MATLAB environment. The last part is the analysis of human, chimpanzee and mice genes.
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Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
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Bioinformatics of human genome
Kupková, Karolína ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with DNA segments containing only adenine and guanine. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There are basic informations about chimpanzees and the human genome and conformations of the chains containing adenine with guanine. The practical part consists of a program that searches for the required sections in sequence, it displays and saves it. The thesis includes analysis of genes which are common for humans and chimpanzees, which were analyzed to determine randomness, functionality a preserving of these sections.
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