Modified bases in tRNA: The structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxyinethyluridine (2), were determined from three-dimensional x-Ray diffraction data, and refined to R=0.036 and R=0.047, respectively. Compound 1 is in the C3′ -endo conformation with X= +5.2° (anti), ψ∞= +63.4° and ψ∞= +180.0° (tt); 2 is in the C2′-endo conformation with X= +49.4° (anti), ψ∞= -60.5° and ψ∞= +60.0° (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3′-stacked tRNA anticodon appears to place 08 within hydrogen bonding istance of the 02′ hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".