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Nanobiophotonics for future health care
Grant agency: GACR
Identification number of grant: P205/12/G118
Head of the project: Prof. Ing. Jiří Homola, CSc., DSc. (Ústav fotoniky a elektroniky AV ČR, v. v. i.)
Vice-head of the project:
Prof. RNDr. Josef Štěpánek, CSc.
Grant annotation
As modern medicine evolves towards quantitative and molecular based science, biophotonics is envisioned to play an increasingly important role in multiple areas of medicine, contributing to quality of health care, reduction of health care costs, and sustainability of the medical care in the ageing society. The proposal aims to advance research in selected areas of nanobiophotonics with focus on photonic molecular biosensors based on plasmonic nanostructures. The main areas of research in this project include research into plasmonic phenomena on metallic nanostructures, development of novel tools for analysis and design of plasmonic nanostructures, fabrication and experimental characterization of plasmonic nanostructures with potential for surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS) sensing, interfacing biomolecules with inorganic nanostructures and investigation of interactions between such biophotonic structures and biological samples, and realization of SPR and SERS biosensors for detection of biomarkers of onco-hematological diseases.
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Nucleic Acid Regulatory Sequences - polymorphism, dynamics, and interactions
Grant agency: GACR
Identification number of grant: 15-06785S
Head of the project: Prof. RNDr. Josef Štěpánek, CSc.
Grant annotation
The project is aimed at detail investigation of structural arrangement, formation of biologically relevant complexes, and dynamics of selected
representative types of nucleic acid regulatory sequences - DNA guanine quadruplexes, miRNA sequences, and DNA transcription elements
containing CArG box – in order to elucidate the molecular mechanism of their regulatory function and its control by external factors, namely
molecular crowding, temperatures and charge compensating molecular surrounding. The nucleic acid segments and/or their complexes with
key proteins will be studied by means of SPR biosensing, Raman and NMR spectroscopy, CD spectroscopy, Raman optical activity, and
molecular dynamics simulations. These methods will be optimized and the experimental and theoretical approaches further developed for
advanced investigation of nucleic acids.
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UV resonance Raman scattering of nucleic acids
Grant agency: GAUK
Identification number of grant: 691412
Head of the project: RNDr. Jakub Klener, Ph.D.
Vice-head of the project:
Prof. RNDr. Josef Štěpánek, CSc.
Grant annotation
The project is focused on determination of secondary and tertiary
structures of nucleic acids (NA) and their interactions. Considering the
requirement of measurements in natural aqueous environment, Raman
spectroscopy (RS), which is capable of acquiring basic information about
the structure and structural changes of NA and their complexes, is very
convenient for that purpose. The disadvantage of standard RS with
visible excitation is the necessity of high NA concentration and the
problems with contamination of samples by low-molecular impurities.
These difficulties can be overcome by using resonance Raman scattering
(RRS) with excitation in the long-wavelength NA absorption band. Because
of substantially higher demands on the apparatus, its adjustment and
employment of measuring schemes that protect the sample from
photodegradation, this technique is only rarely used in NA studies.
The main task of the project will be, besides building up the UV RRS
spectrometer and development of suitable procedures for handling with UV
photosensitive samples, to find out RRS markers sensitive to NA
conformation and its interaction. These findings will be applied in a
subsequent study of particular NA structural motives, important for the
transfer and expression of genetic information.
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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.
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Formation and dynamics of nucleic acid motifs involved in regulation of gene expression
Grant agency: GACR
Identification number of grant: 202/09/0193
Head of the project: Prof. RNDr. Josef Štěpánek, CSc.
Vice-head of the project:
Ing. Ivan Rosenberg, CSc. (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.),
Prof. Ing. Jiří Homola, CSc., DSc. (Ústav fotoniky a elektroniky AV ČR, v. v. i.),
Michaela Vorlíčková (Biofyzikální ústav, Akademie věd České republiky, v.v.i.)
Grant annotation
The project will deal with properties of important nucleic acids (NA)
segments from the viewpoint of their structural fluctuations and
formation or decay kinetics of structural motifs and/or their complexes.
Main accent will be put on employment of a large set of advanced
experimental techniques including micro-Raman spectroscopy, sensors
based on surface plasmon resonance (SPR), and dynamic NMR measurements
on 13C-labeled nucleotides, complemented by molecular dynamics
simulations. Investigation will be concentrated to several families of
NA structural motifs significant for natural and/or artificial
regulation of gene expression. Besides deep understanding of structural
and dynamic properties of the natural and chemically modified NA motifs,
important development and improvement of certain experimental techniques
will be achieved; in particular development of mixing microfluidic
system for kinetic micro-Raman measurements and implementation of a new
concept of SPR imaging with polarization contrast for highly
parallelized measurements.
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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.
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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.
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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
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Izopolární fosfonátové oligonukleotidy jako alternativa fosforothioátových při regulaci exprese genomu
Grant agency: GACR
Identification number of grant: 203/05/0827
Head of the project: Ing. Ivan Rosenberg, CSc. (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.)
Vice-head of the project:
Prof. RNDr. Josef Štěpánek, CSc.
Grant annotation
None
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Neinvazivní fyzikální diagnostika molekulárních interakcí při regulaci genové exprese
Grant agency: GACR
Identification number of grant: 202/05/0628
Head of the project: Prof. RNDr. Josef Štěpánek, CSc.
Grant annotation
None
