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Covalent geometry of nucleic acids
Schramlová, Barbora ; Černý, Jiří (advisor) ; Dohnálek, Jan (referee)
IV Abstract Nucleic acids (NA) are substances that play a fundamental role in all living organisms. They store genetic information and control the process of protein synthesis. These macromolecules are composed of chains of nucleotides. According to the type of sugar in the nucleotides, nucleic acids are divided into DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid). Nucleotide sequences also determine the spatial conformations of nucleic acids. At the level of dinucleotides, conformations are described by classes of dinucleotide conformers - NtC. To study nucleic acids, it is crucial to determine their spatial arrangement. The most common method of three-dimensional observations is X-ray crystallography, which uses the interaction of X-rays with the electron cloud of atoms in the crystal. The result is crystallographic data, which further goes through the process of refinement and validation. One of the essential requirements for reliable refinement and validation are stereochemical standards. These are vocabularies that characterize specific bond lengths, bond angles, torsion angles, planes, and chirality. These parameters were last updated in 2020, but their quality still needs to be improved. This work focuses on the detailed characterization and description of the covalent geometry of nucleic...
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Nucleic Acid Geometry Standards
Schramlová, Barbora ; Černý, Jiří (advisor) ; Dohnálek, Jan (referee)
IV Abstract Nucleic acids (NA) are biochemical macromolecular substances essential for all living organisms - their function is to store genetic information and control the process of protein biosynthesis. Nucleic acids are composed of polynucleotide chains. According to the composition of these, we distinguish two basic types of nucleic acids: DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid). Based on the internal nucleotide sequence and external interactions, these chains are formed into different spatial conformations. At the dinucleotide level, these conformations are described and classified by so-called classes of dinucleotide conformers - NtC. The X-ray crystallography method has been used for over 50 years to reveal the three- dimensional structures of biological macromolecules. The principle of this is the interaction of X-rays with the electron cloud of atoms in the crystal. Atomic positions are then determined based on the calculated electron density. However, with the resolution available for most macromolecular crystals, these crystallographic data are not sufficient to derive a chemically acceptable structure, so stereochemical restraints apply. Stereochemical restraints are dictionaries describing specific bond lengths, bond angles, torsion angles, planes, and chirality. Using these...
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