"Synthesis and Characterization of the Native Anticodon Domain of E. coli tRNALys:  Simultaneous Incorporation of Modified Nucleosides mnm5s2U, t6A, and Pseudouridine Using Phosphoramidite Chemistry"

Mallikarjun Sundaram, Pamela F. Crain, and Darrell R. Davis



Published 2000-07-08 in J. Org. Chem. volume pp 5609–5614 .

Pubmed ID: 10970299
DOI identifier: 10.1021/jo000338b

Abstract:
The anticodon domain of E. coli tRNALys contains the hypermodified nucleosides mnm5s2U and t6A at positions 34 and 37, respectively, along with a more common ψ at position 39. The combination of these three nucleotides represents one of the most extensively modified RNA domains in nature. 2-Cyanoethyl diisopropylphosphoramidites of the hypermodified nucleosides mnm5s2U and t6A were each synthesized with protecting groups suitable for automated RNA oligonucleotide synthesis. The 17 nucleotide anticodon stem-loop of E. coli tRNALys was then assembled from these synthons using phosphoramidite coupling chemistry. Coupling efficiencies for the two hypermodified nucleosides and for pseudouridine phosphoramidite were all greater than 98%. A mild deprotection scheme was developed to accommodate the highly functionalized RNA. High coupling yields, mild deprotection, and efficient HPLC purification allowed us to obtain 1.8 mg of purified RNA from a 1 μmol scale RNA synthesis. Our efficient synthetic protocol will allow for biophysical investigation of this rather unique tRNA species wherein nucleoside modification has been shown to play a role in codon-anticodon recognition, tRNA aminoacyl synthetase recognition, and programmed ribosomal frameshifting. The human analogue, tRNALys,3, is the specific tRNA primer for HIV-1 reverse transcriptase and has a similar modification pattern


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