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Nucleic Acids Research, 1978, Vol. 5, No. 3 893-903
© 1978

Articles

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

Helen M. Berman, Deborah Marcu, Poojappan Narayanan*, John D. Fissekis and Robert L. Lipnick

The Institute for Cancer Research, 7701 Burholme Avenue Philadelphia, PA 19111 Memorial Sloan Kettering Cancer Center New York, NY 10021, USA

Received January 9, 1978.

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), {psi}{infty}= +63.4° and {psi}{infty}= +180.0° (tt); 2 is in the C2'-endo conformation with X= +49.4° (anti), {psi}{infty}= -60.5° and {psi}{infty}= +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".

*Present address: Biochemistry Department, S.U.N.Y. at Stony Brook, NY 11794 USA


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