Book of Abstracts: Albany 2003
June 17-21 2003
NMR Structure Determination of the Anticodon Stem-Loop of Escherichia coli tRNAPhe
The main goal of our work is to understand the structural and thermodynamic effect of base modification on RNA and the cumulative effect of multiple modified bases within one RNA. We are using the ACSLPhe of Escherichia coli to examine the modifications: (N6)-dimethylallyl of residue A37 and pseudouridine at the positions U32 and U39 (Figure 1).
We have found that conversion of A37 to i6A37, catalyzed by the MiaA enzyme, destabilizes the loop structure (1). Co(NH3)63+ induces the formation of a stable U-turn conformation in i6A37-ACSLPhe, but not in unmodified ACSLPhe. Pseudouridylation of U32 stabilizes the stem and has little effect on the loop structure. ψ32 base pairs with A38 and has an anti-configuration about the glycosidic bond. In the double modified molecule ψ32i6A37-ACSL, a destabilizing effect of the dimethylallyl modification at A37 is not compensated by the presence of ψ32.