Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of cis Watson-Crick A/G Base Pairs: The Role of Nonplanar Guanine Amino Group

Systematic X-ray database, phylogenetic and ab initio quantum chemical analysis of molecular interactions and conservation patterns of cis W.C. A/G base pairs in 16S rRNA, 23S rRNA and other available molecules was carried out. In cis W.C. A/G basepairs, the A and G nucleotides interact with their Watson-Crick edges with glycosidic bonds oriented cis relative to each other. The base pair is stabilised by two in plane hydrogen bonds, the C1'-C1' distance is enlarged and the N2(G) guanine amino group is left unpaired. Quantum chemical calculations show that, in absence of other interactions, the unpaired N2(G) of the cis W.C. A/G base pair is substantially nonplanar due to its partial sp3 pyramidalization while the whole base pair is internally propeller twisted and very flexible. The unique molecular properties of the cis W.C. A/G base pairs make them distinct from other base pairing patterns. Crystallographic and phylogenetic data reveal that cis W.C. A/G base pairs play crucial roles in natural RNA structures with salient sequence conservation patterns. The cis W.C. A/G base pairs mostly occur at the ends of canonical helices, where they serve as interfaces between the helix and other motifs, such as bulged bases, internal or hairpin loops, or junctions. Notably, the key contribution to conservation is provided by the unpaired N2(G) guanine amino group that is involved in a wide range of tertiary and neighbour contacts in the available crystal structures. The anomalous C1'-C1' distance appears to be considerably less important in this respect. Many of the key N2(G) contacts are actually oriented out of the plane of the guanine base and thus actively utilise the partial sp3 pyramidalization of the N2(G) amino nitrogen. There in general is a lack of A/G to G/A covariation which, except of the N2(G) position, would at first sight be entirely isosteric. On contrary, there is a frequent occurrence of G/A to G/U covariation, as G/U wobble base pair has unpaired amino group in the same position as the cis-W.C. G/A one. The cis W.C. A/G base pairs are typically not conserved when the N2(G) is not involved in any significant interaction. Obtaining the proper picture of the interactions and phylogenetic patterns of the cis W.C. A/G base pairs requires a detailed analysis of the link between the molecular structures and the energetics of interactions at a level of single H-bonds and contacts, combining the experimental data with advanced theoretical analysis.

J. Sponer1,2
A. Mokdad4
J. E. Sponer1
N. Spackova2
J. Leszczynski3
N.B. Leontis

1Institute of Biophysics
Academy of Sciences of the Czech Republic and National Center for Biomolecular Research
Kralovopolska 135
612 65, Brno, Czech Republic
Phone: (420) 5415 17133
Fax: (420) 5412 11293
2J. Heyrovsky Institute of Physical Chemistry
Academy of Sciences of the Czech Republic
Dolejskova 3
182 23 Prague, Czech Republic
3Department of Chemistry
Computational Center for Molecular Structure and Interactions
Jackson State University
Jackson, Mississippi 39217, USA
4Chemistry Department and Center for Biomolecular Sciences
Bowling Green State University
Bowling Green, OH 43403
Phone: 419 372 8663
Fax: 419 372 9809