A5090321403- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- Spectroscopy Techniques in Biomedical and Chemical Research
- RNA and protein synthesis mechanisms
- Spectroscopy and Chemometric Analyses
- Electrospun Nanofibers in Biomedical Applications
- Porphyrin and Phthalocyanine Chemistry
- Conducting polymers and applications
- Mediterranean and Iberian flora and fauna
- Operations Management Techniques
- Hemoglobin structure and function
- Plant Taxonomy and Phylogenetics
- Scientific Measurement and Uncertainty Evaluation
- Historical, Literary, and Cultural Studies
- Origins and Evolution of Life
- Spectroscopy and Quantum Chemical Studies
- Advanced Sensor and Energy Harvesting Materials
- African Botany and Ecology Studies
- Photoreceptor and optogenetics research
- Microbial Inactivation Methods
- Protein Structure and Dynamics
- Synthesis and Characterization of Heterocyclic Compounds
- Plant and animal studies
- Gas Dynamics and Kinetic Theory
Czech Academy of Sciences, Institute of Biophysics
2012-2023
Czech Academy of Sciences
2023
Charles University
2003-2014
Czech Academy of Sciences, Institute of Physics
2010-2014
Institute of Molecular and Translational Medicine
2014
Palacký University Olomouc
2014
Central European Institute of Technology
2012
Central European Institute of Technology – Masaryk University
2012
DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring concentrations differing orders of magnitude. As Raman spectroscopy can applied samples ranging from those accessible absorption and CD spectroscopies up extremely concentrated solutions, gels even crystals; it used here clarify polymorphism a core telomeric sequence G3(TTAG3)3 in presence K+ Na+ ions throughout...
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich sequences, is reflected by typical changes CD and UV absorption spectra. By means spectroscopic methods, electrophoresis, chemical modifications other procedures, we characterized iM stability sequences with different cytosine block lengths interrupted various numbers types nucleotides. Particular attention was paid to the iMs at pH conditions close neutral. We...
Abstract A semiautomated method combining intensity normalization with effective elimination of the solvent signal and non‐Raman background is presented for Raman spectra biochemical biological analytes in aqueous solutions. The particularly suitable rapid effortless preprocessing extensive datasets taken as a function gradually varied physicochemical parameters, e.g. analyte and/or ligand concentration, temperature, pH, pressure, ionic strength, time, etc. For normalization, strong OH...
Abstract Cytosine-rich DNA regions can form four-stranded structures based on hemi-protonated C.C+ pairs, called i-motifs (iMs). Using CD, UV absorption, NMR spectroscopy, and DSC calorimetry, we show that model (CnT3)3Cn (Cn) sequences adopt iM under neutral or slightly alkaline conditions for n > 3. However, the iMs are formed with long-lasting kinetics these melt significant hysteresis. Sequences 6 in two more separate steps, indicating presence of different species, proportion...
Abstract Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that frequently found in genomes. The stability G4s depends, among other factors, on the number G‐tetrads. Three‐ or four‐tetrad and antiparallel two‐tetrad have been characterized experimentally; however, existence an intramolecular (i. e., not dimeric multimeric) parallel‐stranded DNA G4 has never experimentally observed. Many sequences compatible with can be important genomic regions, such as promoters, for which...
A bstract In this work, we demonstrate the underused potential of Raman spectroscopy in detecting formation DNA G‐quadruplex (G4) and differentiating between various G4‐folding topologies. As model structures, used a 22‐mer human telomere fragment AG 3 (TTAG ) (denoted here as wt its two variants with adenine abasic lesions at position 19 ( ap19 or positions 7, 13, ap7‐13‐19 ), structures which were previously characterized. These oligonucleotides adopt three basic G4‐folds: basket‐type form...
In the present work, real ability of a confocal Raman microspectroscopy to monitor chemical composition vacuoles within living yeast cells was investigated and critically assessed. Simple, economical, practical protocols immobilization suitable for less laborious, high‐throughput, spatially resolved measurements were tested their possible impacts on physiological states viability cells. We have demonstrated that, acquiring spectra from statistically sound sets immobilized employing advanced...
The catalytic activity of a heme‐based oxygen sensor phosphodiesterase from Escherichia coli ( Ec DOS ) towards cyclic di GMP is regulated by the redox state heme iron complex in enzyme's sensing domain and association external ligands with center. Specifically, Fe( II more active than III complex, its further enhanced O 2 or CO binding. In order to determine how coordination atom regulate , we investigated flexibility isolated N‐terminal heme‐binding ‐heme) monitoring spectral properties at...
Abstract The intercalated motif (iM) is a four‐stranded structure consisting of two parallel homoduplexes formed by hemiprotonated C.C + pairs and antiparallel to each other. iM generally at acidic pH, as cytosine protonation required for its formation. However, sequences with long tracts can form physiological pH conditions. Here, we use both off‐resonant Raman UV‐resonant (using synchrotron radiation) spectroscopy (RS) study the sequence (C 9 T 3 ) C , which has been recently thoroughly...
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Abstract Silicate glasses are ubiquitous on terrestrial planets wherever molten rock – generated by volcanism or impacts is quenched air water. Hence, they provided ready and abundant reactive solid surfaces for prebiotic chemistry the early Earth. Here, we show that glass composition determines basicity, which in turn modulates outcome of synthetic processes such as polymerization 3’, 5’ cyclic guanosine monophosphate.