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The relationship of thermodynamic stability at a G[bull ]U recognition site to tRNA aminoacylation specificity

Published online by Cambridge University Press:  01 November 1999

PETER STRAZEWSKI ,
EWA BIALA ,
KAY GABRIEL  and
WILLIAM H. McCLAIN
PETER STRAZEWSKI
Affiliation:
Institute of Organic Chemistry, University of Basel, CH–4056 Basel, Switzerland
EWA BIALA
Affiliation:
Institute of Organic Chemistry, University of Basel, CH–4056 Basel, Switzerland Permanent address: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
KAY GABRIEL
Affiliation:
Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin 53706-1567, USA
WILLIAM H. McCLAIN
Affiliation:
Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin 53706-1567, USA
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Abstract

The G[bull ]U pair at the third position in the acceptor helix of Escherichia coli tRNAAla is critical for aminoacylation. The features that allow G[bull ]U recognition are likely to include direct interaction of alanyl-tRNA synthetase with distinctive atomic groups and indirect recognition of the structural and stability information encoded in the sequence of G[bull ]U and its immediate context. The present work investigates the thermodynamic stability and acceptor activity for a comprehensive set of variant RNAs with substitutions of the G[bull ]U pair of E. coli tRNAAla. The four RNAs with Watson–Crick substitutions had a lower acceptor activity and a higher stability relative to the G[bull ]U RNA. On the other hand, the RNAs with mispair substitutions had a lower stability, but either a higher or a lower acceptor activity. Thus, the entire set of variant RNAs does not exhibit a correlation between thermodynamic stability of the free, unbound tRNA and its acceptor activity. The substantial acceptor activity of tRNAs with particular mispair substitutions may be explained by their ability to assume the conformational preferences of alanyl–tRNA synthetase. Moreover, the G[bull ]U pair may provide a point of deformability for the substrate tRNA to adapt to the enzyme's active site.

Keywords

mid-point temperaturesprotein synthesistRNA identitywobble base pair
Type
REPORTS
Information
RNA , Volume 5 , Issue 11 , November 1999 , pp. 1490 - 1494
Copyright
1999 RNA Society

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