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HDO Raman spectrum
Šubr, Martin ; Štěpánek, Josef (advisor) ; Procházka, Marek (referee)
Title: HDO Raman spectrum Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor: Prof. RNDr. Josef Štěpánek, CSc., Institute of Physics of Charles University Abstract: The main aim of this thesis is to determine the HDO Raman spectrum. This spectrum cannot be measured separately in its liquid form, but it is possible to obtain it by a specific mathematical processing of sets of measured spectra with different H/D ratios. In this work we measured Raman spectra of liquid water with different mole fractions of water and heavy water, which were evaluated by factor analysis. Except for well-known spectra of water and heavy water, spectrum of HDO was determined. For fitting of this spectrum and its analysis, model with equilibrium constant and linear correction of the spectral shape with respect to the relative ratio of D was used. Keywords: Raman scattering, water and heavy water, HDO, factor analysis
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Improved determination of DNA duplex stability by using UV spectroscopy
Víšová, Ivana ; Štěpánek, Josef (advisor) ; Kočišová, Eva (referee)
This work deals with determination of thermodynamic parameters concerning the temperature induced decomposition of DNA duplexes. Precise temperature dependences of solution UV absorption spectra have been measured for several concentrations. Proposals and tests of various data analysis procedures, with aim to find out optimal way how to determine the thermodynamic potentials changes, represent the core of the work. It has been demonstrated that the combination of a factor analysis and a fit of thermodynamic equations to temperature dependences of obtained coefficient values, enables these parameters to be obtained from a measurement performed for only one concentration and with better precision than by using the so far recommended method based on a melting temperature determination for several concentrations.
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Geometry and stability study of nucleic acids distinctive single-strand motifs
Říhová, Martina ; Štěpánek, Josef (advisor) ; Mašek, Vlastimil (referee)
Subject of this thesis is the regulatory DNA segment, the so-called Serum Response Element (SRE), which possesses highly specific structural characteristics and its structural flexibility plays probably a key role in its physiological activity. Structural properties of 16-mer SRE segments capable to form hairpin structures were studied by means of accurate measurements of temperature dependent Raman spectra. Due to the close connection of oligonucleotide chain structural stability with the stacking interaction, temperature dependent Raman and UV absorption spectra were measured on dinucleotides serving as a simple model system for the stacking investigation. The measurements results processed by factor analysis provided characteristic spectral patterns and confirmed that stacking interaction depends on the base order. By fitting the thermodynamic equilibrium equations to the factor analysis outputs, the thermodynamic characteristics of the thermally induces structural changes in hairpinforming complexes were estimated and difference spectra characterizing opened and closed hairpins, which enable the further specification of the geometry of these complexes, were obtained.
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Vibrational modes of nucleic acids components characterized by means of variable proton-deuterium exchange
Zoul, David ; Štěpánek, Josef (advisor) ; Šloufová, Ivana (referee)
Although the nucleon acid oscillatory spectra have been studied for a long period of time, many of oscillating modes have not been properly explained regarding their geometric sensitivity and weak binding. One of the possibilities how to acquire experimental data for interpretation of theese modes is to confront oscillating spectra of isotopes. The simplest is proton - deutron exchange. When molecules dissolve in heavy water they rapidly exchange the heteroatoms, but this is simultaneous for more stages, which leads to dynamic equilibrium state among various isotope forms. Statistic analysis of temporal progression of Raman spectra give us the possibility to analyze the spectra and to obtain unique experimental data. This technique is very promising for more complex nucleon acid segments to gain more structural information. This diploma thesis represents pilot study of introduced methodics. The objective is to implement adaptation of Raman spectrometr for given types of expiments and undertake first series of measurements. The results should clarify application bounds of proposed method refering to sensitivity, time constant of incident isotope exchange, severity of read-out in comparasion of achieved accuracy of the measurement.
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Function of Magnesium Ions in the Formation of Biologically-Active Nucleic Acids Structures
Espinoza Herrera, Shirly Josefina ; Štěpánek, Josef (advisor) ; Mašek, Vlastimil (referee) ; Setnička, Vladimír (referee)
ESPINOZA HERRERA S.J. - DOCTORAL THESIS - FUNCTION OF MAGNESIUM IONS IN THE FORMATION OF BIOLOGICALLY-ACTIVE NUCLEIC ACIDS STRUCTURES ____________________________________________________________________ ABSTRACT Interaction of magnesium ions, the divalent ions with the highest concentration inside living cells, with the key biomolecules of nucleic acids was studied with aim to find out structural details of the interaction mechanism and effect of the magnesium ions presence on the nucleic-acid structure and structural transitions. Raman spectroscopy was chosen as the main experimental method, some complementary measurements of UV absorption spectra were also performed. Basic analyses of the spectral series obtained as a function of temperature and/or for various concentrations of Mg2+ ions were done by means of factor analysis. Where possible the factor analysis outputs were used for fits of appropriate thermodynamic equations. For the studies, various nucleic-acid molecular models were employed, in particular complementary RNA homopolynucleotides polyA and polyU, DNA homopolynucleotides polydA and polydT and RNA 14-mer oligonucleotide representing the apical hairpin of the TAR segment of HIV-1 genomic RNA. We have confirmed via Raman spectroscopy that magnesium ions added to a solution of polyA-polyU...
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Microcalorimetric determination of RNA triplex thermodynamic stability
Říhová, Martina ; Štěpánek, Josef (advisor) ; Kočišová, Eva (referee)
Nazcv prace: Mikrokalorimelricke slanovcni termodynamicke stability triplexu RNA Autor: Martina Rihova Kaledra (ustav): Fyzikalni ustav UK Vcdouci bakalafske prace: Prof. RNDr. Josef Stcpanck, Csc. e-mail vedouciho: stepjosiyj;karlov.mff.cuni.cz Abstrakt: Prace je zamC'fena na urcovani termodynamickych charaktcristik duplexu a triplexu ribonukleove kyscliny. Rozpad a v/nik komplexu hyl sledovan na diferencnim skcnovacim mikrokalorimelru. Jako vzorky byly pouzity smesne ro/toky syntelicky pfipravenych homopolymerii RNA, polyA a polyU, o ruznych stcchiometrickych pomerech. Z namcfenych dal byly urceny termodynamickc paramclry komplexu, tcdy odpovidajici zmeny entalpie AH a entropic AS a teplola tani komplexu. Vysledky ukazaly, /e pfi techto mcfcnich dochazi k systematickc /mene namerenych charakteristik pfi opakovanych scanech. Tento jcv patrnc souvisi s intcrakci RNA s povrchem mefici kyvcty a jc tedy zavazny z hlediska aplikovatclnosli scanovaci mikrokalorimctric pro pfesna kvantitativni tennodynamicka studia ribonukleove kyscliny. Zmcny teploty tani zpusobenc pridanim hofciku do rozloku uka/aly, zc jeho ucinkem so pfi pfipojeni ifctiho vlakna k duplexu RNA komplex stabilizuje. Klicova slova: triplex RNA, duplex RNA, mikrokalorimetric, termodynamickc charakteristiky, teplota tani. Title: Microcalorimetric...
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