Report No xxxx - Instytut Fizyki JÄ drowej PAN

STRUCTURAL ANALYSIS OF RNA DUPLEXES CONTAINING
ADENOSINE BULGES BY NMR SPECTROSCOPY
Łukasz Popenda 1 , Zofia Gdaniec 1 , Grażyna Dominiak 1 , Jan Milecki 2 , Ryszard W. Adamiak 1
1 Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14,
61 704 Poznań, Poland; 2 Department of Chemistry, Adam Mickiewicz University
Grunwaldzka 6, 60-780 Poznań, Poland
Double stranded regions of RNA molecules contain structural motifs, in which one or
more residues in one strand does not have the pairing residue in the opposite strand. Bulges
are the simplest as well as the most abundant structural motifs that play a crucial structural
and functional role in many RNAs [1]. At present, bulges are known to participate in the
process of RNA folding, RNA-RNA and RNA-protein interactions [2].
Previous thermodynamic studies on the influence of bulges on RNA duplexes stability
[3] has resulted in the following observations: (i) all the bulges destabilise the duplexes, (ii)
bulges containing the same number of A and U residues destabilise RNA duplexes to the
same extent, (iii) long bulges not necessarily destabilise the duplex more than the shorter
ones. Up to now, no systematic structural studies on the preferable conformation of these
RNA motifs have been done. This is important to emphasize that very often bulged structures
that are obtained from X-ray analysis differ from those determined in solution by NMR
spectroscopy. This fact is an additional reason for doing the structural studies in solution.
The subject of our research are bulged RNA duplexes containing unpaired adenine
residues. Analysis of homo- and heteronuclear NMR spectra (2D NOESY, DQF-COSY, 1 H-
13 C HSQC, 1 H- 31 P HSQC) let us to conclude about the structure and dynamics of RNA
duplexes with single- and trinucleotide bulges. Our data show that the bulged residues within
RNA duplexes containing single bulged adenosine, tend to stack into the helix. The
experimental data reveal that the accommodation of bulged adenine residue between the
neighbouring base pairs, does not disturbe the regular A-RNA structure. Analysis of NMR
spectra and the thermodynamic data obtained for the duplex with three bulged adenine
residues show that the presence of additional residues within the bulged region causes a
considerable destabilisation of the duplex structure.
Literature:
[1] M. E. Burkard, D. H.Turner, I. Tinoco Jr. in: RNA World II, R. Gesteland, T. Cech, and J.
Atkins (ed), Cold Spring Harbor Press, 1999, str. 233
[2] T. Hermann, D. J. Patel, Structure, 8 (2000), 47
[3] C. E. Longfellow, R. Kierzek, D. H. Turner, Biochemistry, 29 (1990) 278
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