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Národní NMR centrum Josefa Dadoka

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Head of Core Facility
Researcher ID
Telefon: +420 54949 3771
Mobil: 774436880
E-mail: ,
Kancelář:

Dedication

The Centre is named after Professor Josef Dadok, a pioneer of nuclear magnetic resonance spectroscopy in Czechoslovakia and an important figure in the NMR instrumentation and methodology worldwide.

prof_dadokIn the 1950s, Josef Dadok and his team at the Czechoslovak Academy of Sciences developed instruments for high resolution NMR spectroscopy. Based on his design, Tesla Brno Company started industrial production of NMR spectrometers in 1965, making Czechoslovakia only the third country in the world (after the U.S. and Japan) to master the production of this sophisticated instrumentation.

Since late 1960s, Josef Dadok worked and lived in the USA where he became professor of chemical instrumentation at Carnegie Mellon University in Pittsburgh, PA. Among his accomplishments there is a development of the first 600 MHz (14.1 T) magnet suitable for high resolution NMR spectroscopy in 1970s.

For his achievements, Professor Josef Dadok was awarded doctor honoris causa degree by Masaryk University in 2013.


Main Activity

Core Facility of High Field NMR Spectroscopy provides access to NMR spectrometers in the range of proton frequencies from 500 MHz to 950 MHz. The equipment is suited mainly to the studies of structure, dynamics and interactions of biomolecules, i.e. proteins, nucleic acids and carbohydrates. However, the instrumentation is flexible enough to cover also various research needs in material science, organic and inorganic chemistry, biochemistry, biology and biophysics.

Unique Features

NMR (Nuclear Magnetic Resonance) spectroscopy is a key technology for research in modern life sciences allowing detailed investigation of biomolecular structure and dynamics at the atomic level, both in solutions and in solid state. The successful application of NMR in biology requires multidisciplinary approach combining knowledge in biochemistry, molecular biology, quantum physics, electronics, data analysis, and computational chemistry. The high-end instrumentation and the team of experienced researchers will ensure expert services, user training, and the cost-effective use of resources both for internal and external users. Benefits include access to state-of-the-art high-field NMR instrumentation and support in processing, analysis and interpretation of the experimental data. External user projects will be selected by peer review on the basis of scientific merit, technical suitability and feasibility. The centre will also offer training enabling non-specialists to develop the necessary skills.

Services and Methodologies Provided

  • Measurement of NMR spectra at magnetic fields ranging from 11.75 T to 22.35 T (corresponding to 1H frequencies 500 MHz to 950 MHz)
  • Consultation of choice and setup of multidimensional experiments, data processing, and evaluation strategies
  • Measurement and processing of multidimensional spectra (with up to five dimensions) of proteins using non-uniform sampling methods
  • Measurements of complete sets of very small residual dipolar couplings (RDCs) and evaluation of their accurate values supported by in-house software
  • Cross-validation of RDCs in nucleic acid bases, peptide planes, and protein secondary structure elements
  • 3D structure calculations, validation of structure/restraints
  • Measurement, evaluation, and interpretation of relaxation data describing intramolecular motions
  • Ab-initio calculation of NMR parameters, molecular dynamics simulations

Key Equipment

  • 950 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids, 4 RF channels, 5 mm triple-resonance (1H-13C-15N) inverse cryoprobe with cooled 1H and 13C preamplifiers, sample temperature range −40ºC to 80ºC
  • 850 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids, 4 RF channels, 5 mm triple-resonance (1H/19F-13C-15N) inverse cryoprobe with cooled 1H and 13C preamplifiers, sample temperature range 0ºC to 135ºC.
  • 700 MHz NMR spectrometer Bruker Avance III HD for biomolecular applications, 4 RF channels, 5 mm triple-resonance (1H-13C-15N) cryoprobe optimized for 13C detection with cooled 1H, 13C and 15N preamplifiers, sample temperature range −40ºC to 80ºC
  • 700 MHz NMR spectrometer Bruker Avance III HD for multinuclear applications in liquids and solids, 4 RF channels, equipped with a 5 mm dual broad-band probe, 5 mm dual inverse broad-band probe, 1.7 mm triple resonance (1H-13C-15N) probe, 3.2 mm solid-state triple-resonance (1H-13C-15N) MAS probe, and a 4.0 mm solid-state dual CP/MAS probe
  • 600 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids, 5 RF channels, quadruple-resonance (1H-31P-13C-15N) inverse cryoprobe with cooled 1H and 13C preamplifiers, sample temperature range −40ºC to 80ºC
  • 500 MHz NMR spectrometer Bruker Avance for multinuclear applications in liquids and solids, 3 RF channels, equipped with a 5 mm nitrogen-cooled dual (BB-1H) cryoprobe (Prodigy), 5 mm room temperature triple-resonance (1H-13C-15N) probe, 10 mm dual (13C, 1H) probe, and a 4 mm solid-state dual (BB-1H) CP/MAS probe

The Core Facility is part of Czech National Affiliated Centre of INSTRUCT.

All CEITEC core facilities are available to external users (academia and companies). Czech and international researchers from universities and research institutes interested in accessing core facilities can benefit from support of research infrastructure CIISB, funded by the Ministry of Education, Youth and Sports of the Czech Republic. International researchers can also benefit from support of Project iNext.

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seznam / vizitky

Jméno a pozice

E-mail

Telefon

doc. RNDr. Radovan Fiala, CSc.
Vedoucí výzkumný pracovník
+420 54949 3771
RNDr. Otakar Humpa
Výzkumný pracovník
+420 54949 4508
Mgr. Petr Padrta, Ph.D.
Výzkumný pracovník
+420 54949 6355
Mgr. Jaromír Toušek, Dr.
Výzkumný pracovník
+420 54949 7032
Mgr. Jan Novotný, Ph.D.
Výzkumný pracovník – postdoc
+420 54949 2620

VYBRANÉ PUBLIKACE

2017

  • KEJNOVSKA, I; BEDNAROVA, K; RENCIUK, D; DVORAKOVA, Z; SKOLAKOVA, P; TRANTIREK, L; FIALA, R; VORLICKOVA, M; SAGI, J, 2017:Clustered abasic lesions profoundly change the structure and stability of human telomeric G-quadruplexes. NUCLEIC ACIDS RESEARCH 45 (8), p. 4294 - 4305.
  • POSTULKOVA, H; CHAMRADOVA, I; PAVLINAK, D; HUMPA, O; JANCAR, J; VOJTOVA, L, 2017:Study of effects and conditions on the solubility of natural polysaccharide gum karaya. FOOD HYDROCOLLOIDS 67 , p. 148 - 156.

2016

  • MICHLOVSKA, L; VOJTOVA, L; HUMPA, O; KUCERIK, J; ZIDEK, J; JANCAR, J, 2016:Hydrolytic stability of end-linked hydrogels from PLGA-PEG-PLGA macromonomers terminated by alpha,omega-itaconyl groups. RSC ADVANCES 6 (20), p. 16808 - 16816.
  • TRISKOVA, I; FIALA, R; TRNKOVA, L, 2016:Redox Processes of Guanine Moieties in DNA Heptamers Related to Hydrogen Evolution. ELECTROANALYSIS 28 (11), p. 2841 - 2848.
  • VAVRINSKA, A; ZELINKA, J; SEBERA, J; SYCHROVSKY, V; FIALA, R; BOELENS, R; SKLENAR, V; TRANTIREK, L, 2016:Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions (vol 64, pg 53, 2016). JOURNAL OF BIOMOLECULAR NMR 65 (1), p. 49 - 49.
  • VAVRINSKA, A; ZELINKA, J; SEBERA, J; SYCHROVSKY, V; FIALA, R; BOELENS, R; SKLENAR, V; TRANTIREK, L, 2016:Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 64 (1), p. 53 - 62.

PROJEKTY

  • iNEXT - Infrastructure for NMR, EM and X-ray crystallography for translational research (653706), H2020 - Excellent science - Research Infrastructures, 2015 - 2019
  • CIISB4HEALTH - Česká infrastruktura pro integrativní strukturní biologii pro lidské zdraví (CZ.02.1.01/0.0/0.0/16_013/0001776), MEYS, 2017 - 2021
  • CIISB - České centrum pro integrativní strukturní biologii (LM2015043), MEYS, 2016 - 2019
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Equipment Research group / CF Profile card
500 MHz NMR spectrometer Bruker Avance for multinuclear applications in liquids and solids 500 MHz NMR spectrometer Bruker Avance for multinuclear applications in liquids and solids
CF: Josef Dadok National NMR Centre
600 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids 600 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids
CF: Josef Dadok National NMR Centre
700 MHz NMR spectrometer Bruker Avance III HD for biomolecular applications 700 MHz NMR spectrometer Bruker Avance III HD for biomolecular applications
CF: Josef Dadok National NMR Centre
700 MHz NMR spectrometer Bruker Avance III HD for multinuclear applications in liquids and solids 700 MHz NMR spectrometer Bruker Avance III HD for multinuclear applications in liquids and solids
CF: Josef Dadok National NMR Centre
850 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids 850 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids
CF: Josef Dadok National NMR Centre
950 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids 950 MHz NMR spectrometer Bruker Avance III HD for high resolution spectroscopy in liquids
CF: Josef Dadok National NMR Centre
Seznam služeb
Others
Quality control 1H NMR is a suitable method for detecting impurities such as solvent residues and it is widely used in the pharmaceutical, medical, and food industries for quality control. Our laboratory is equipped for measuring liquid and solid samples, and is capable of providing measurements of a wide range of elements. Within the service, we offer measurements of elements 1H, 13C, 15N, 31P, 19F and others with higher resonance frequencies than 15N.

Booking of the service is available via CEITEC intranet system
Compound identification The NMR spectrum reflects connection between atoms in the molecule which makes the method ideally suited for identification of compounds. Even subtle differences in molecular configuration can be distinguished relatively easily. The method can be applied to both synthetic and natural compounds.

Booking of the service is available via CEITEC intranet system
NMR structural analysis in liquids Based on quantification of spin-spin couplings and nuclear Overhauser effect intensities, a complete 3D structure of compounds can be solved. However, the procedure may be laborious. Ask for details if you are interested.

Booking of the service is available via CEITEC intranet system
Biomolecular structure and dynamics by NMR Proteins of up to 200 amino acids, nucleic acids up to 50 nucleotides can be studied. The necessary concentrations are at least 0.1 mM for simple tests, 0.5 mM for more complex studies. Much depends on the molecular weight, folding etc. For solving 3D structures, isotope labeling with 15N and 13C is always needed for proteins and for oligonucleotides larger that approximately 30 nucleotides. Specialized methods, some of them developed in our laboratory, for charactering intrinsically disordered proteins (IDPs) are available. We can measure spectra with up to 5 dimensions to assign the protein backbone and sidechain resonances.

Booking of the service is available via CEITEC intranet system
NMR analysis in solid state 1D CP MAS spectra of 13C, 15N, 27Al, 29Si, 31P. The application of solid-state NMR techniques usually arises due to specific interest in the physics of solid state, including packing effects and polymorphic structures. Solid-state NMR can be also used to study chemical shielding anisotropy. Sometimes, the application is motivated by an inability to dissolve the material of interest.

Booking of the service is available via CEITEC intranet system
Sample requirements (organic chemistry) Solubility in one of the solvents suitable for NMR spectroscopy http://www.chem.wisc.edu/areas/reich/handouts/nmr/nmr-solvents.htm Preferably D2O, CDCl3, DMSO-d6, benzene-d6, methanol-d4, acetone-d6, N,N-dimethyl formamide-d7 and Dichloromethane-d7. Approximate minimal concentrations of samples are 0.1 mM for 1H spectra and 10 mM for 13C spectra (corresponding 0.015 mg and 1.5 mg respectively, based on molecular weight 300 and sample volume 0.5 ml).

Booking of the service is available via CEITEC intranet system
Tasks NOT suitable for NMR Low sample quantities – the sensitivity of NMR is inherently low. Therefore, the method is NOT suitable for analysis if only very low quantity of sample is available. See Sample requirements above for minimal required concentrations. Large numbers of samples – no sample changer available (yet). We are not equipped for tasks requiring advanced statistical evaluation of large series of spectra such as metabolomics. No ‘low gamma’ probes available – we have no equipment for measuring nuclei with resonance frequencies lower than 15N (50.66 MHz at 11.75 T field – 500 MHz spectrometer)

Booking of the service is available via CEITEC intranet system
Training There is a number of NMR courses of various levels available in IS MU. A solid theoretical background of NMR spectroscopy is covered in the course C5320 Fyzikálně chemické základy NMR (in Czech). Practical training in measuring NMR spectra with a special attention to biomolecules (proteins, nucleic acids) is provided in the course C7995 Practical NMR Spectroscopy of Biomolecules (in English). Check the Information System for the other courses. To use the spectrometer in the Centre independently without supervision by a more experienced spectroscopist you have to pass a course C7995 or similar and be examined by the core facility staff. Then you can get access to the booking system and user account will be created for you at the spectrometers.

Booking of the service is available via CEITEC intranet system
1H NMR (Proton nuclear magnetic resonance) The most basic experiment is a simple one-dimensional proton NMR spectrum. 1H NMR is a suitable method for purity control, analysis of mixtures and confirmation of molecular structure. It is widely used in the pharmaceutical, medical, and food industries for quality control. The experiment is highly sensitive and measurement time is short. Simple NMR spectra are recorded in solution, and solvent protons must not be allowed to interfere. Deuterated (symbolized as D) solvents for the specific use in NMR are preferred. The most common solvents used include deuterated water, D2O, deuterated acetone, (CD3)2CO, deuterated methanol, CD3OD, deuterated dimethyl sulfoxide, (CD3)2SO, and deuterated chloroform, CDCl3. Approximate minimal concentrations of samples are 0.1 mM for 1H (corresponding 0.015 mg, based on molecular weight 300 and sample volume 0.5 ml). Deuterated solvents permit the use of deuterium frequency-field lock (deuterium lock) to eliminate the effect of the natural drift of the NMR's magnetic field. Proton NMR spectra of most organic compounds are characterized by chemical shifts in the range +15 to -4 ppm and by spin-spin coupling between protons. The integration curve for each proton reflects the abundance of the individual protons.

Booking of the service is available via CEITEC intranet system
13C NMR (carbon nuclear magnetic resonance) For most organic compounds, information on the number and character of the carbon is essential for confirmation and proof of their structure. As the most common carbon isotope 12C does not possess magnetic moment, NMR spectroscopy relies on 13C whose natural abundance is only 1.1%. This, combined with four times lower gyromagnetic ratio compared to 1H, results in much lower measurement sensitivity than in the case 1H NMR and the measurements are therefore more time-consuming. Routine 13C NMR spectra are measured usually with broadband proton decoupling and sensitivity enhancement (3x) by NOE effect. In our CF, a very sensitive cryoprobe (175 MHz at 16.45 T) is available for the measurement of 13C -NMR, which significantly reduces the measurement times (tens of minutes instead of hours). In analogy to proton NMR, 13C NMR allows the identification of carbon atoms in an organic molecule just as proton NMR identifies hydrogen atoms. As such, 13C NMR is an important tool in chemical structure elucidation in organic chemistry. From a 1H -decoupled carbon (13C) spectrum useful information about 13C chemical shifts is obtained. Alternatively, carbon multiplicity and 1H-13C coupling constants can be determined from the gated decoupled methodology and quantitative measurements can be made from the inverse gated experiments. Assignment of the 13C spectrum is usually performed with the help of additional NMR methods. As a general strategy: Carbon multiplicity is determined from 1D APT or DEPT experiments. Correlation with 1H nuclei via 1J(CH) is achieved from HSQC or HMQC-type experiments. Correlation with 1H nuclei via nJ(CH) is achieved from HMBC-type experiments.

Booking of the service is available via CEITEC intranet system
13C NMR structure characterization of polyolefines Quantitative measurement of 13C NMR spectra is performed in our laboratory using a 10 mm dual 13C-{1H} NMR probehead on the NMR Bruker AVANCE III 500 spectrometer at the field of 11.74 T (500 MHz and 125 MHz for 1H and 13C nuclei, respectively). The analysis of the NMR data enables to characterize various polyolefins such: 13C NMR structure characterization of polyethylene (HDPE, LDPE, LLDPE): determination of comonomer(s), number of side chain branches 13C NMR characterization of poly(ethylene-propylene) block and random copolymers: calculation of ethylene and propylene content, sequence length distribution 13C NMR tacticity characterization of polypropylene at the level of pentads The detailed analysis of these NMR data is performed by Polymer Institute Brno. www.polymer.cz

Booking of the service is available via CEITEC intranet system
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