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Structure and Dynamics of Nucleic Acids
People involved:
Staff:
Prof. RNDr. Vladimír Sklenář, DrSc.
RNDr. Radovan Fiala, CSc.
Mgr. Lukáš Žídek, Ph.D.
Mgr. Petr Padrta, Ph.D.
Diploma, Ph.D. and postdoctoral fellows:
Bc. Pavel Kadeřávek
Mgr. Petr Novák
Project description:
Nucleic acids are compounds of essential importance
for all living organisms. Although the general structural features of regular
DNAs and RNAs are well known, there exist a plethora of structural motifs
different from the regular double helix. Detailed knowledge of the structural
characteristics is necessary for understanding their biological function. NMR
spectroscopy allows studying the structures of nucleic acids oligomers in
solution at close to physiological conditions . The structures of d(C4G4)
and
d(G4C4) duplexes and
d(GCGAAGC) hairpin were
among those solved in our laboratory.
In order to delineate the relationships
between the structures, thermodynamic stabilities and biological function of
nucleic acids it is highly desirable to complement the structural studies by
characterization of equilibrium conformational fluctuations. Measurement of
nuclear spin relaxation by NMR spectroscopy is a powerful approach for studying
intramolecular motions at atomic resolution on the nanosecond to picosecond time
scale. We have studied the dynamics of two
RNA hairpins
containing UUCG and GCAA tetraloops by 15N and 13C relaxation.
Figure 1:
Schematic representation of the internal dynamics of a tetradecamer RNA hairpin containing GCAA tetraloop. The study was based on 13C NMR relaxation data.
Diploma and Ph.D. theses offered:
List of selected publications:
- Žídek, L.; Štefl, R.; and Sklenář, V. 2001. NMR methodology for the study of
nucleic acids. Curr. Opin. Struct. Biol. 11: 275 - 281.
- Trantírek, L.; Štefl, R.; Vorlíčková, M.; Koča, J.; Sklenář, V.; Kypr,
J. 2000. An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose
Rings. J. Mol. Biol. 297: 907 - 922.
- Štefl, R.; Trantírek, L.; Vorlíčková, M.; Koča, J.; Sklenář, V.; Kypr,
J. 2001. A-like Guanine-Guanine Stacking in the Aqeuous DNA Duplex of d(GGGGCCCC).
J. Mol. Biol. 307: 513 - 524.
- Padrta, P.; Štefl, R.; Králík, L.; Žídek, L.; Sklenář, V. 2002. Refinement
of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar
couplings. J. Biomol. NMR 24: 1 - 14.
- Akke, M.; Fiala, R.; Jiang, F.; Patel, D.; Palmer, A. G. 1997.
Base dynamics in a UUCG tetraloop RNA hairpin characterized by N-15 spin
relaxation: Correlations with structure and stability. RNA 3: 702 - 709.
Cooperations:
- Juli Feigon, University of California, Los Angeles, USA
- Samuel E. Butcher, University of Wisconsin, Madison, USA
Financial sources:
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