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Study of DNA hydration by analysis of structural data from databases
Šrůtková, Alžběta ; Schneider, Bohdan (advisor) ; Hoksza, David (referee)
The deoxyribonucleic acids play an essential role in the living organisms by storing the genetic information. The process of the genetic information transfer, translation and transcription is carried out by other molecules, mostly proteins, which cause DNA bend and locally deform. These protein-DNA interactions, together with the nucleotide sequence, result in different DNA conformations. The description and classification of the DNA local structural diversity at a level of dinucleotides is provided by so-called dinucleotide conformer classes, NtC. The NtC classification system developed for description of the local conformations of nucleic acids consists of 97 NtC classes. In this work we use 44 classes important for the description of DNA conformations. All biomolecules, including DNA are heavily hydrated. The first hydration layer around DNA is largely localized. The structure of this hydration layer depends on the sequence and conformation of the analyzed biomolecule. The DNA structural classification by the NtC classes allows specific study of the first hydration layer with a sufficient sequence and structural granularity. Based on the data available in the structural databases, we studied hydration of double helical tetranucleotide fragments in the three biologically most important DNA conformational...
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