Geometry and stability study of nucleic acids distinctive single-strand

Author: Mgr. Martina Říhová
Supervisor: Prof. RNDr. Josef Štěpánek, CSc.
Type: Master

Abstract: Subject of this thesis is the regulatory DNA segment, the so called Serum Response Element (SRE), which possess highly specific structural characteristics. Previous research results imply this segment is capable of hairpin forming and its structural flexibility plays key role in its physiologic activity. The accurate thermally dependent measurements of 16-mer SRE segments were provided by Raman spectroscopy. Due to structural stability close connection with stacking interaction the temperature dependent Raman and UV absorbtion spectra on dinucleotides as a model system for stacking investigation were provided. The measurements results were processed by factor analysis and showed that stacking interaction depend on base order. Providing a fit according to thermodynamic equilibrium equations the thermodynamic characteristics of the thermally induces structural changes in hairpin-forming complexes were stated and difference spectra characterizing opened and closed hairpins, which enable the further specification of the geometry of these complexes, could be calculated.

Keywords: DNA hairpin, Raman spectroscopy, SRE, komplex stability, dinucleotides