Experimentální a bioinformatické stanovení fyzikálně chemických a strukturních vlastností nukleových kyselin

Svoboda, Jakub

In this work, I present the DNATCO web tool and its practical use in the refinement of crystal structures of 18-mer DNA oligonucleotides. DNATCO serves for simple and rapid annotation and validation of nucleic acid structures using dinucleotide conformational classes - NtC. To this end, it utilizes several unique tools such as RSCC/RMSD plots combining information about the fit of the model to its experimental density and similarity to representatives defining NtC classes. Additional improvements include visualization of NtC classes and base pairing at several levels, analysis of valence geometry, and generation of extended mmCIF and restraint files. The entire application runs in the user's browser thanks to its architecture, thereby achieving security and privacy while eliminating the need for user account management. Finally, the user interface has been redesigned into a modern form. I have used the tools in solving crystal structures of DNA containing non-canonical base pairs in the central region. Despite the necessity of manual interventions, I achieved improvements in local geometry and conformational fit for several low- resolution structures while maintaining the fit to experimental density.

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