Novel Experimental Techniques in Nuclear Magnetic Resonance of Biomolecules
Prof. RNDr. Vladimír Sklenář, DrSc.
RNDr. Radovan Fiala, CSc.
Mgr. Lukáš Žídek, Ph.D.
A general goal of NMR studies of biomolecules is to obtain as accurate as possible
data that can characterize the structure and/or dynamics of the studied system.
A necessary first step in any NMR study is the resonance assignment. For this
purpose, the methods that rely on through-bond interactions are preferable.
Methods to allow complete resonance assignment of both proteins and nucleic
acids have been developed by now. Today, the task is to
sensitivity and resolution of the methods to allow application to
bimolecular systems of increasing complexity.
No matter how sophisticated assignment methods may be, the structure calculations relied up to recently
mostly on restraints derived from NOE spectra that include only local
interactions. Therefore, additional sources of structural constraints are being
investigated such as residual dipolar couplings and structural dependence of
either isotropic chemical shifts or chemical shift anisotropy. New efficient
methods are therefore needed to
measure small changes in spin-spin
couplings induced by oriented media and to obtain accurate values of
chemical shifts of as many nuclei in the molecule as possible.
Example of a pulse scheme for a two-dimensional NMR experiment. The scheme shown is for the HCNC experiment proposed for establishing connectivities between H8 and C4 in the purine bases and between H6 and C2 in the pyrimidine bases of nucleic acids (Fiala et al. J. Biomol. NMR 2004 29: 477-490).
Diploma and Ph.D. theses offered:
List of selected publications:
- Fiala, R.; Jiang, F.; Sklenář, V. 1998. Sensitivity optimized HCN and HCNCH
experiments for C-13/N-15 labeled oligonucleotides. J. Biomol. NMR 12: 373 - 383.
- Fiala, R.; Czernek, J.; Sklenář, V. 2000. Transverse relaxation optimized
triple-resonance NMR experiments for nucleic acids. J. Biomol. NMR 16: 291 - 302.
- Sklenář, V., et al. 1998. Optimization of triple-resonance HCN experiments for
application to larger RNA oligonucleotides. J. Magn. Reson. 130: 119 - 124.
- Žídek, L., et al. 2001. Measurement of small scalar and dipolar couplings in
purine and pyrimidine bases. J. Biomol. NMR 21: 153 - 160.
- Fiala, R.; Munzarová, M. L.; Sklenář, V. 2004.
Experiments for Correlating Quaternary Carbons in RNA Bases. J. Biomol. NMR 29: 477-490.
- Juli Feigon, University of California, Los Angeles, USA
- Samuel E. Butcher, University of Wisconsin, Madison, USA