Finished grants:

  • Molecular mechanisms of DNA regulatory segment recognition by MADS box family transcription factors

    Grant agency: GAUK
    Identification number of grant: 402111
    Head of the project: Mgr. Barbora Řezáčová
    Vice-head of the project: Prof. RNDr. Josef Štěpánek, CSc., Mgr. Pavla Ottová, RNDr. Václav Profant

    Grant annotation
    This project is focused on study of physico-chemical properties and formation of complexes between the MADS-box family transcription factors and the DNA regulatory segment. The aim of the project is to elucidate the functional role of the MADS-box in the specific recognition of the CArG-box CC (A/T)6GG containing DNA segment. Geometry and dynamics of model oligomers, protein, and their complex will be characterized by spectroscopic techniques, in particular Raman and UV absorption spectroscopy, both stationary and time-resolved fluorescence measurements including stopped-flow method and fluorescence anisotropy decay. To complete the thermodynamic characteristics, microcalorimetric measurements (DSC) will be employed. Within the first year of the project, the effect of environmental conditions, mainly pH, temperature, and presence of selected cations, on the conformational stability of the model oligonucleotides, protein and protein-oligonucleotide complex will be determined and the impact of the MADS-box complex formation with the target DNA segment on its Raman spectrum, fluorescence emission and fluorescence anisotropy will be described. Next stage of the project solution will be devoted to dynamics study of the DNA segment, model proteins, and their complexes by fluorescence anisotropy decay measurement of both the intrinsic fluorophores (Tyr) and fluorescence labels and/or probes.

  • TAR and DIS segments of HIV-1 RNA: structural stability of hairpins and their complexes with potential aptamers

    Grant agency: GAUK
    Identification number of grant: 50910
    Head of the project: Mgr. Pavla Ottová
    Vice-head of the project: Prof. RNDr. Josef Štěpánek, CSc., Mgr. Barbora Řezáčová

    Grant annotation
    The project is devoted to experimental structural-stability study of key HIV–1 hairpins. Analyzing temperature dependences of Raman spectra and results of complementary UV absorption and microcalorimetric measurements, the stabilizing effect of magnesium ions on the structure of the TAR hairpin, its R06 aptamer and their kissing complex will be determined. This will elucidate the physico-chemical conditions for a successful inhibition of the regulation TAR-hairpin function by means of aptamer strategy. Next task of the project, which will be solved during following years, is to characterize the temperature dependence of the DIS hairpin and its potential aptamers structure and to compare the formation and stability of kissing complexes formed both by a couple of DIS hairpins and by the DIS hairpin and its aptamer. Also the effect of magnesium ions on the stabilization of the DIS hairpin and its complexes will be uncovered.

  • Structural and physical properties of the complexes formed by RNA hairpins and chemically modified aptamers

    Grant agency: GAUK
    Identification number of grant: 147507
    Head of the project: Mgr. Jan Vachoušek
    Vice-head of the project: Prof. RNDr. Josef Štěpánek, CSc., Mgr. Pavla Ottová, Mgr. Barbora Řezáčová

    Grant annotation
    Study of RNA hairpins properties has a strong implication mainly for antisense therapies, since the RNA hairpins perform important functions namely in the replication cycle of retroviruses, including HIV. Among the most studied RNA hairpins belongs TAR and DIS hairpins that can be found in HIV viral RNA. Functionality of the RNA hairpins can be successfully blocked by chemically modified antisense aptamers that show to have a potential to open another door leading to the suppression of HIV epidemic in the future. Successful design of efficient antisense aptamers requires knowledge of the structure and properties of the RNA hairpins as well as of their antisense aptamers. This task will be solved by means of Raman spectroscopy, UV spectroscopy and other additional methods.

  • Spektroskopická a molekulárně–dynamická charakterizace mechanismu interakce Ribonukleázy H s hybridním DNA/RNA duplexem.

    Grant agency: GAUK
    Identification number of grant: 257688
    Head of the project: RNDr. Martin Kříž, Ph.D.
    Vice-head of the project: Prof. RNDr. Josef Štěpánek, CSc., Mgr. Pavla Ottová, Mgr. Barbora Řezáčová

    Grant annotation
    None